A confounding effect of missing data on character conflict in maximum likelihood and Bayesian MCMC phylogenetic analyses.

No abstract is available for this paper.

• Publication year

  2014

• Venue

  Molecular Phylogenetics and Evolution

• Publication date

  2014-11-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1016/j.ympev.2014.08.021PMID 25173567
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Roderick J. Little and Donald B. Rubin: Statistical Analysis with Missing Data

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• Limitations of locally sampled characters in phylogenetic analyses of sparse supermatrices.

  2014influential reference
• Divergent maximum-likelihood-branch-support values for polytomies.

  2014cited by this paper
• Novel information theory-based measures for quantifying incongruence among phylogenetic trees.

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• Phylogenetic Bias in the Likelihood Method Caused by Missing Data Coupled with Among-Site Rate Variation: An Analytical Approach

  2014cited by this paper
• Disparate parametric branch-support values from ambiguous characters.

  2014influential reference
• Dubious resolution and support from published sparse supermatrices: the importance of thorough tree searches.

  2014cited by this paper
• Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads

  2014cited by this paper
• Quantification and relative severity of inflated branch-support values generated by alternative methods: an empirical example.

  2013cited by this paper
• A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

  2013cited by this paper
• Identification and characterization of a previously undescribed family of sequence-specific DNA-binding domains

  2013cited by this paper
• An artifact caused by undersampling optimal trees in supermatrix analyses of locally sampled characters.

  2013cited by this paper
• MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

  2012influential reference
• Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data.

  2012influential reference
• Misleading results of likelihood‐based phylogenetic analyses in the presence of missing data

  2012influential reference
• Supermatrices, supertrees and serendipitous scaffolding: inferring a well-resolved, genus-level phylogeny of Styphelioideae (Ericaceae) despite missing data.

  2012cited by this paper
• Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes

  2011cited by this paper
• The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees.

  2011cited by this paper
• Spurious 99% bootstrap and jackknife support for unsupported clades.

  2011cited by this paper
• New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

  2010influential reference
• The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference

  2009cited by this paper
• Empirical Likelihood in Missing Data Problems

  2009cited by this paper
• Unringing a bell: metazoan phylogenomics and the partition bootstrap

  2009cited by this paper
• Coalescent methods for estimating phylogenetic trees.

  2009cited by this paper
• Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment?

  2008cited by this paper
• Parsimony and explanatory power

  2008cited by this paper
• TNT, a free program for phylogenetic analysis

  2008cited by this paper
• PAML 4: phylogenetic analysis by maximum likelihood.

  2007influential reference
• Application of phylogenetic networks in evolutionary studies.

  2006cited by this paper
• Parsimony and Bayesian phylogenetics

  2006cited by this paper
• RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

  2006cited by this paper
• The limits of conventional cladistic analysis

  2006cited by this paper
• Quantification of the success of phylogenetic inference in simulations

  2006influential reference
• Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative.

  2006cited by this paper
• Hidden likelihood support in genomic data: can forty-five wrongs make a right?

  2005cited by this paper
• Phylogenetic MCMC Algorithms Are Misleading on Mixtures of Trees

  2005cited by this paper
• Strange bayes indeed: uniform topological priors imply non-uniform clade priors.

  2005cited by this paper
• Treatment of multiple trees in resampling analyses

  2004cited by this paper
• PAUP* [Phylogenetic Analysis Using Parsimony (and Other Methods)]

  2004influential reference
• The Logical Basis of Phylogenetic Analysis

  2004cited by this paper
• Prospects for Building the Tree of Life from Large Sequence Databases

  2004cited by this paper
• Character‐state space versus rate of evolution in phylogenetic inference

  2004cited by this paper
• Does Adding Characters with Missing Data Increase or Decrease Phylogenetic Accuracy ?

  2003cited by this paper
• The challenge of constructing large phylogenetic trees.

  2003cited by this paper
• Missing data, incomplete taxa, and phylogenetic accuracy.

  2003cited by this paper
• Obtaining maximal concatenated phylogenetic data sets from large sequence databases.

  2003cited by this paper
• Resolution of a supertree/supermatrix paradox.

  2002cited by this paper
• Resolution of a Supertree / Supermatrix Paradox

  2002cited by this paper
• Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics

  2002cited by this paper
• Heterotachy, an important process of protein evolution.

  2002cited by this paper
• An approximately unbiased test of phylogenetic tree selection.

  2002cited by this paper
• Molecular polytomies.

  2001cited by this paper
• CONSEL: for assessing the confidence of phylogenetic tree selection

  2001cited by this paper
• Philosophy and phylogenetic inference: a comparison of likelihood and parsimony methods in the context of Karl Popper's writings on corroboration.

  2001cited by this paper
• Philosophy and Phylogenetic Inference: A Comparison of Likelihood and Parsimony Methods in the Context of Karl Popper's Writings on Corroboration

  2001cited by this paper
• Methods for Quick Consensus Estimation

  2001cited by this paper
• Linked branch support and tree stability.

  2000cited by this paper
• From Gene Trees to Species Trees

  2000cited by this paper
• Comments on Allard and Carpenter (1996), or the Aquatic Ape Hypothesis Revisited

  1999cited by this paper
• Long‐Branch Abstractions

  1999cited by this paper
• Corroboration among Data Sets in Simultaneous Analysis: Hidden Support for Phylogenetic Relationships among Higher Level Artiodactyl Taxa

  1999cited by this paper
• Phylogenetic supertrees: Assembling the trees of life.

  1998cited by this paper
• Does adding characters with missing data increase or decrease phylogenetic accuracy?

  1998cited by this paper
• SplitsTree: analyzing and visualizing evolutionary data

  1998cited by this paper
• Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences.

  1998cited by this paper
• Bamboozled again! Inadvertent isolation of fungal rDNA sequences from bamboos (Poaceae: Bambusoideae).

  1997cited by this paper
• Multiple sources of character information and the phylogeny of Hawaiian drosophilids.

  1997cited by this paper
• Recombinant DNA sequences generated by PCR amplification.

  1997cited by this paper
• Is the Felsenstein zone a fly trap?

  1997cited by this paper
• Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method.

  1997influential reference
• Links between maximum likelihood and maximum parsimony under a simple model of site substitution.

  1997cited by this paper
• The phylogenetic position of Rhopalura ophiocomae (Orthonectida) based on 18S ribosomal DNA sequence analysis.

  1996cited by this paper
• ON SIMULTANEOUS ANALYSIS

  1996cited by this paper
• Gene Trees and Species Trees: Molecular Systematics as One-Character Taxonomy

  1992cited by this paper
• Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA

  1992cited by this paper
• Substitutional bias confounds inference of cyanelle origins from sequence data

  1992cited by this paper
• A Concern for Evidence and a Phylogenetic Hypothesis of Relationships among Epicrates (Boidae, Serpentes)

  1989cited by this paper
• CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP

  1985cited by this paper
• Analysis of Taxonomic Congruence among Morphological, Ecological, and Biogeographic Data Sets for the Leptopodomorpha (Hemiptera)

  1980cited by this paper
• Evolution of Protein Molecules

  1979cited by this paper
• Cases in which Parsimony or Compatibility Methods will be Positively Misleading

  1978cited by this paper
• Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters

  1973cited by this paper
• An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution

  1970cited by this paper
• CHAPTER 24 – Evolution of Protein Molecules

  1969cited by this paper
• Quantitative Phyletics and the Evolution of Anurans

  1969influential reference

• Over‐reliance on Completeness exposes ultraconserved elements datasets to non‐randomly distributed missing data

  2026cites this paper
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• The new problem of Chinlestegophis and the origin of caecilians (Amphibia, Gymnophionomorpha) is highly sensitive to old problems of sampling and character construction

  2024cites this paper
• A phylogenomic tree of wood-warblers (Aves: Parulidae): Dealing with good, bad, and ugly samples.

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• Twenty-five well-justified fossil calibrations for primate divergences

  2023cites this paper
• Treefrog Diversity in the Neotropics: Phylogenetic Relationships of Scinaxini (Anura: Hylidae: Hylinae)

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• Appendage-Bearing Sordariomycetes from Dipterocarpus alatus Leaf Litter in Thailand

  2023cites this paper
• Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches.

  2023cites this paper
• Phylogeny of iguanodontian dinosaurs and the evolution of quadrupedality

  2022cites this paper
• Phylogenetic analysis of Middle-Late Miocene apes.

  2022cites this paper
• RUNNING HEADER: Missing data produces biased loci TITLE: Uneven missing data skews phylogenomic relationships within the lories and lorikeets

  2021cites this paper
• Assessing topological congruence among concatenation-based phylogenomic approaches in empirical datasets.

  2021cites this paper
• X-chromosomal STR based genetic polymorphisms and demographic history of Sri Lankan ethnicities and their relationship with global populations

  2021cites this paper
• The phylogeny of robber flies (Asilidae) inferred from ultraconserved elements

  2021cites this paper
• Parsimony analysis of phylogenomic datasets (I): scripts and guidelines for using TNT (Tree Analysis using New Technology)

  2021cites this paper
• Total evidence and sensitivity phylogenetic analyses of egg‐brooding frogs (Anura: Hemiphractidae)

  2020cites this paper
• The phylogeny of the Casque‐headed Treefrogs (Hylidae: Hylinae: Lophyohylini)

  2020cites this paper
• Phylogeny Estimation Given Sequence Length Heterogeneity

  2020cites this paper
• Bayesian Tip-dated Phylogenetics in Paleontology: Topological Effects and Stratigraphic Fit.

  2020cites this paper
• Ultraconserved elements help resolve the phylogeny of an ancient radiation of venomous flies (Diptera: Asilidae)

  2020cites this paper
• Species delimitation of North American Nyssa species

  2020cites this paper
• Tip-dating and the origin of Telluraves.

  2019cites this paper
• Straight From the Plastome: Molecular Phylogeny and Morphological Evolution of Fargesia (Bambusoideae: Poaceae)

  2019cites this paper
• Evidence of Absence Treated as Absence of Evidence: The Effects of Variation in the Number and Distribution of Gaps Treated as Missing Data on the Results of Standard Maximum Likelihood Analysis

  2019cites this paper
• Likelihood approximations of implied weights parsimony can be selected over the Mk model by the Akaike information criterion

  2019cites this paper
• Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses.

  2019cites this paper
• Divergence and support among slightly suboptimal likelihood gene trees

  2019cites this paper
• Which morphological characters are influential in a Bayesian phylogenetic analysis? Examples from the earliest osteichthyans

  2019cites this paper
• Split-inducing indels in phylogenomic analysis

  2018cites this paper
• Resolving Relationships among the Megadiverse Butterflies and Moths with a Novel Pipeline for Anchored Phylogenomics

  2018cites this paper
• Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting.

  2018cites this paper
• Revised classification and phylogeny of an Afrotropical species group based on molecular and morphological data, with the description of a new genus (Coleoptera: Scarabaeidae: Onthophagini)

  2017influential citation
• RADseq dataset with 90% missing data fully resolves recent radiation of Petalidium (Acanthaceae) in the ultra‐arid deserts of Namibia

  2017cites this paper
• An updated phylogeny and infrageneric classification of the genus Sisyrinchium (Iridaceae): Challenges of molecular and morphological evidence

  2017cites this paper
• To include or not to include: The impact of gene filtering on species tree estimation methods

  2017cites this paper
• Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction

  2017cites this paper
• A morphological supermatrix‐based phylogeny for the Neotropical fish superfamily Anostomoidea (Ostariophysi: Characiformes): phylogeny, missing data and homoplasy

  2016influential citation
• Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes).

  2016cites this paper
• Virus evolution during chronic hepatitis B virus infection as revealed by ultradeep sequencing data.

  2016cites this paper
• Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids.

  2016influential citation
• Phylogenomics for Systematic Biology.

  2016cites this paper
• The Impact of Missing Data on Species Tree Estimation.

  2016cites this paper
• Population genetic study of 34 X-Chromosome markers in 5 main ethnic groups of China

  2015cites this paper
• Do missing data influence the accuracy of divergence-time estimation with BEAST?

  2015cites this paper
• Molecular Phylogenetics and Evolution

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