Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous

By Bryan D. Kolaczkowski, Joseph W. Thornton. Nature, 2004

603 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/5021d974ea52c834188ae25d5f0ebb9c92aebca7

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Citations in the corpus

Taxon sampling and the accuracy of phylogenetic analyses (2008, background): “…estimation has been shown to be inconsistent in the presence of severe branch-length heterogeneity (heterotachy, a form of non-stationarity) if the substitution process is assumed to be homogeneous across all lineages (Kolaczkowski & Thornton, 2004; Spencer et al., 2005; Philippe et al., 2005).”
Implied weighting and its utility in palaeontological datasets: a study using modelled phylogenetic matrices (2016, neutral): “…methods (such as likelihood and Bayesian inference) to phylogenetic analysis of morphological data is at present still far from ubiquitous (Kolaczkowski & Thornton 2004; Lee & Worthy 2011; Wright & Hillis 2014), parsimony is currently the most widespread option for palaeontological…”
Application of phylogenetic networks in evolutionary studies. (2006, neutral): “The example in Kolaczkowski and Thornton (2004) demonstrates that unaccounted rate variation can mislead both maximum likelihood (ML) and parsimony-based analyses into selecting the wrong tree.”
Innovation and cultural transmission in the American Paleolithic: Phylogenetic analysis of eastern Paleoindian projectile-point classes (2014, background): “…the criterion for valuating a topology—the probability of the data, given the tree—is calculated with ference to an explicit evolutionary model from which the data are assumed to be istributed identically (Kolaczkowski and Thornton, 2004). p W o a e re d guide to phylogenetic relationships.”
IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING? (2009, background): “…of systematists because of the related issue of heterotachy the change in rate of characters or sites over time (Kolaczkowski and Thornton 2004, 2008) and also because they can generate unexpected phylogenetic signals in DNA sequence datasets (Kolaczkowski and Thornton 2004; Matsen and Steel 2007).”
A review of long‐branch attraction (2005, background): “The only simulation study that has touched upon the subject would be the recent work by Kolaczkowski and Thornton (2004), where two simulated partitions with differing properties were combined and showed the advantage for parsimony relative to likelihood-based methods, but the opposite…”
Selecting optimal partitioning schemes for phylogenomic datasets (2014, methodology): “We note that the approach we have implemented here, using a rate multiplier and a single set of molecular branch lengths, does not allow for heterotachy (variation in the pattern of rates among sites over time), although this is known to be an important source of variation in patterns of substitutio”
Phylogenetic Analyses of Basal Angiosperms Based on Nine Plastid, Mitochondrial, and Nuclear Genes (2005, background): “The most effective and efficient ways to analyze the resulting large matrices remain parsimony methods, which have been shown to be robust even when data are heterogeneous (Kolaczkowski and Thornton 2004).”
Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices (2016, background): “2002), that is, when evolutionary rates vary over time, leads to systematic errors in phylogenetic reconstruction (Kolaczkowski and Thornton 2004; Philippe et al. 2005).”
Ultrafast Approximation for Phylogenetic Bootstrap (2013, background): “…models, other types of model violations such as polytomies and heterotachy (i.e., varying substitution rates among different tree branches and alignment sites) (Lopez et al. 2002) are known to cause systematic bias in the ML and Bayesian methods (Kolaczkowski and Thornton 2004; Lewis et al. 2005).”
Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots (2010, methodology): “For example, using models that fail to account for the heterogeneous patterns of sequence evolution that are inherent in such large data sets can mislead ML analyses (29).”
Molecular evidence that phoronids are a subtaxon of brachiopods (Brachiopoda: Phoronata) and that genetic divergence of metazoan phyla began long before the early Cambrian (2005, background): “Despite the apparent reliability and robustness of the results, there remain potential and fundamental problems with available methods of phylogenetic inference (Kolaczkowski and Thornton 2004) which caution us to remember that conclusions like those presented here are but hypotheses, open to refuta”
Detecting and overcoming systematic errors in genome-scale phylogenies. (2007, background): “Known causes of model violations are across-site rate variation (Yang, 1994), heterotachy (the across-site rate variation through time) (Kolaczkowski and Thornton, 2004; Philippe et al., 2005c; Spencer et al., 2005), site-interdependent evolution (Robinson et al.”