2007/04/18 by F. A. Matsen, Frederick A. Matsen, Matsen, Frederick A. +2
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · #Evolution and Paleontology Studies #FOS: Biological sciences #Genetic diversity and population structure #Genomics and Phylogenetic Studies #Populations and Evolution (q-bio.PE) #q-bio.PE
paper · pdf · doi:10.48550/arxiv.0704.2260
openalex publication_date 2007/04/18 · arxiv created 2007/06/30 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent debate. Much of the controversy stems from simulations of mixture model data on a given tree topology for which reconstruction algorithms output a tree of a different topology; these findings were held up to show the shortcomings of particular tree reconstruction methods. In so doing, the underlying assumption was that mixture model data on one topology can be distinguished from data evolved on an unmixed tree of another topology given enough data and the ``correct'' method. Here we show that this assumption can be false. For biologists our results imply that, for example, the combined data from two genes whose phylogenetic trees differ only in terms of branch lengths can perfectly fit a tree of a different topology.