Resampling Residuals on Phylogenetic Trees: Extended Results

Abstract

In this article the results of Waddell and Azad (2009) are extended. In particular, the geometric percentage mean standard deviation measure of the fit of distances to a phylogenetic tree is adjusted for the number of parameters fitted to the model. The formulae are also presented in their general form for any weight that is a function of the distance. The cell line gene expression data set of Ross et al. (2000) is reanalyzed. It is shown that ordinary least squares (OLS) is a much better fit to the data than a Neighbor Joining or BME tree. Residual resampling shows that cancer cell lines do indeed fit a tree fairly well and that the tree does have strong internal structure. Simulations show that least squares tree building methods, including OLS, are strong competitors with BME type methods for fitting model data, while real world examples often suggest the same conclusion.

9 pages, 2 figures, 2 tables

References in corpus (2)

• Combinatorics of least squares trees
• Resampling Residuals: Robust Estimators of Error and Fit for Evolutionary Trees and Phylogenomics

Cited by in corpus (6)

• Homo denisova, Correspondence Spectral Analysis, Finite Sites Reticulate Hierarchical Coalescent Models and the Ron Jeremy Hypothesis
• New g%AIC, g%AICc, g%BIC, and Power Divergence Fit Statistics Expose Mating between Modern Humans, Neanderthals and other Archaics
• Extended Distance-based Phylogenetic Analyses Applied to 3D Homo Fossil Skull Evolution
• An Algorithmic Pipeline for Analyzing Multi-parametric Flow Cytometry Data
• Expanded Distance-based Phylogenetic Analyses of Fossil Homo Skull Shape Evolution
• Complimentary Phylogenetic Signals for Morphological Characters and Quantitative 3D Shape Data within genus Homo