2014/05/26 by Jesús Fernández-Sánchez, Fernández-Sánchez, Jesús, Marta Casanellas +1
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)
paper · pdf · doi:10.48550/arxiv.1405.6546
openalex publication_date 2014/05/26 · openalex created_date 2022/10/04 · openalex updated_date 2026/07/28
One reason why classical phylogenetic reconstruction methods fail to\ncorrectly infer the underlying topology is because they assume oversimplified\nmodels. In this paper we propose a topology reconstruction method consistent\nwith the most general Markov model of nucleotide substitution, which can also\ndeal with data coming from mixtures on the same topology. It is based on an\nidea of Eriksson on using phylogenetic invariants and provides a system of\nweights that can be used as input of quartet-based methods. We study its\nperformance on real data and on a wide range of simulated 4-taxon data (both\ntime-homogeneous and nonhomogeneous, with or without among-site rate\nheterogeneity, and with different branch length settings). We compare it to the\nclassical methods of neighbor-joining (with paralinear distance), maximum\nlikelihood (with different underlying models), and maximum parsimony. Our\nresults show that this method is accurate and robust, has a similar performance\nto ML when data satisfies the assumptions of both methods, and outperforms all\nmethods when these are based on inappropriate substitution models or when both\nlong and short branches are present. If alignments are long enough, then it\nalso outperforms other methods when some of its assumptions are violated.\n