Statistical tests of models of DNA substitution

Cited by (736)

Items 101–200 of 736

1. Combined Support for Wholesale Taxic Atavism in Gavialine Crocodylians
   John Gatesy, George Amato, Mark Allen Norell, Rob DeSalle, Cheryl Y. Hayashi · 2003 · Systematic Biology
2. A Likelihood Ratio Test to Detect Conflicting Phylogenetic Signal
   John P. Huelsenbeck, James J. Bull · 1996 · Systematic Biology
3. Comparative Phylogeography of Mesoamerican Highland Rodents: Concerted versus Independent Response to Past Climatic Fluctuations
   Jack M. Sullivan, Elizabeth Arellano, Duke S. Rogers · 2000 · The American Naturalist
4. Morphology, Molecules, and the Phylogenetics of Cetaceans
   Sharon L. Messenger, Jimmy A. McGuire · 1998 · Systematic Biology
5. Sensitivity of the relative-rate test to taxonomic sampling
   Marc Robinson‐Rechavi, Manolo Gouy, Christian Gautier, Dominique Mouchiroud · 1998 · Molecular Biology and Evolution
6. PHYLOGENETIC STUDIES ON DIDELPHID MARSUPIALS II. NONMOLECULAR DATA AND NEW IRBP SEQUENCES: SEPARATE AND COMBINED ANALYSES OF DIDELPHINE RELATIONSHIPS WITH DENSER TAXON SAMPLING
   Robert S. Voss, Sharon A. Jansa · 2003 · Bulletin of the American Museum of Natural History
7. An Empirical Codon Model for Protein Sequence Evolution
   C. Kosiol, Ian H Holmes, Nick Goldman · 2007 · Molecular Biology and Evolution
8. Phylogenetic relationships of aroids and duckweeds (Araceae) inferred from coding and noncoding plastid DNA
   L. Cabrera, Gerardo A. Salazar, Mark W. Chase, Simon Joseph Mayo, Josef Bogner, Patricia Dávila · 2008 · American Journal of Botany
9. The Prevalence and Impact of Model Violations in Phylogenetic Analysis
   Suha Naser-Khdour, Bùi Quang Minh, Wenqi Zhang, Eric A. Stone, Robert Lanfear · 2019 · Genome Biology and Evolution
10. Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets
    Arong Luo, Huijie Qiao, Yan‐Zhou Zhang, Weifeng Shi, Simon Y. W. Ho, Weijun Xu, Ai‐bing Zhang, Chao‐Dong Zhu · 2010 · BMC Evolutionary Biology
11. Data exploration in phylogenetic inference: scientific, heuristic, or neither
    Taran Grant, Arnold G. Kluge · 2003 · Cladistics
12. Should We Use Model-Based Methods for Phylogenetic Inference When We Know That Assumptions About Among-Site Rate Variation and Nucleotide Substitution Pattern Are Violated?
    Jack M. Sullivan, David L. Swofford · 2001 · Systematic Biology
13. RNA Sequence Evolution With Secondary Structure Constraints: Comparison of Substitution Rate Models Using Maximum-Likelihood Methods
    Nicholas Jon Savill, David C. Hoyle, Paul G. Higgs · 2001 · Genetics
14. Phylogeny of Saxifragales (Angiosperms, Eudicots): Analysis of a Rapid, Ancient Radiation
    Mark Fishbein, Carola Hibsch‐Jetter, Douglas E. Soltis, Larry D. Hufford · 2001 · Systematic Biology
15. Inference of Population History Using a Likelihood Approach
    Gunter Weiss, Arndt von Haeseler · 1998 · Genetics
16. A likelihood method for the detection of selection and recombination using nucleotide sequences
    Nicholas C. Grassly, Edward Charles Holmes · 1997 · Molecular Biology and Evolution
17. Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models
    Maria O. Anisimova, C. Kosiol · 2008 · Molecular Biology and Evolution
18. Systematics of the grey mullets (Teleostei: Mugiliformes: Mugilidae): Molecular phylogenetic evidence challenges two centuries of morphology-based taxonomy
    Jean-Dominique Durand, Kang‐Ning Shen, Wei‐Jen Chen, Brian Wade Jamandre, Hager Blel, K. Diop, Mauro Nirchio, Francisco Javier García-De León, Alan K. Whitfield, C.-W. Chang et al. · 2012 · Molecular Phylogenetics and Evolution
19. Model adequacy and the macroevolution of angiosperm functional traits
    Pennell, Matthew W., FitzJohn, Richard G., Cornwell, William K., Harmon, Luke J. · 2015 · The American Naturalist
20. Phylogeny of carabid beetles as inferred from 18S ribosomal DNA (Coleoptera: Carabidae)
    David R. Maddison, MichaeL. D. BakeR. And, Karen A. Ober · 1999 · Systematic Entomology
21. BEST‐FIT MAXIMUM‐LIKELIHOOD MODELS FOR PHYLOGENETIC INFERENCE: EMPIRICAL TESTS WITH KNOWN PHYLOGENIES
    Cliff Cunningham, Hongxiao Zhu, David M. Hillis · 1998 · Evolution
22. PHYLOGEOGRAPHY AND HISTORY OF GIANT GALAPAGOS TORTOISES
    Adalgisa Caccone, Gabriele Gentile, James P. Gibbs, Thomas H. Fritts, Howard L. Snell, Jessica Betts, Jeffrey R. Powell · 2002 · Evolution
23. Molecular phylogenies and host-parasite cospeciation: gophers and lice as a model system
    Mark S. Hafner, Roderic Page · 1995 · Philosophical Transactions of the Royal Society B Biological Sciences
24. Forty million years of mutualism: Evidence for Eocene origin of the yucca-yucca moth association
    Olle Pellmyr, Jim Leebens‐Mack · 1999 · Proceedings of the National Academy of Sciences
25. The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining.
    John P. Huelsenbeck · 1995 · Molecular Biology and Evolution
26. THE ORIGIN AND DIVERSIFICATION OF GALAPAGOS MOCKINGBIRDS
    Brian S. Arbogast, Sergei V. Drovetski, Robert L. Curry, Peter T. Boag, Gilles Seutin, Peter Raymond Grant, B. Rosemary Grant, David J. Anderson · 2006 · Evolution
27. Tests of applicability of several substitution models for DNA sequence data.
    Andrey Rzhetsky, M Nei · 1995 · Molecular Biology and Evolution
28. Genes under positive selection in Escherichia coli
    Lise Petersen, Jonathan P. Bollback, Matthew W. Dimmic, Melissa J. Hubisz, Rasmus Nielsen · 2007 · Genome Research
29. Model use in phylogenetics: nine key questions
    Scot A. Kelchner, Michael A. Thomas · 2006 · Trends in Ecology & Evolution
30. MONKEYS AND TOADS DEFINE AREAS OF ENDEMISM ON SULAWESI
    Ben J. Evans, Jatna Supriatna, Noviar Andayani, Mohammed Iqbal Setiadi, David C. Cannatella, Don J. Melnick · 2003 · Evolution
31. Hemichordates and deuterostome evolution: robust molecular phylogenetic support for a hemichordate + echinoderm clade
    Lindell D. Bromham, Bernard M. Degnan · 1999 · Evolution & Development
32. Statistical Properties of the Maximum Likelihood Method of Phylogenetic Estimation and Comparison With Distance Matrix Methods
    Ziheng Yang · 1994 · Systematic Biology
33. Bayesian molecular dating: opening up the black box
    Lindell D. Bromham, Sebastián Duchêne, Xia Hua, Andrew M. Ritchie, David Alejandro Duchêne, Simon Y. W. Ho · 2017 · Biological reviews/Biological reviews of the Cambridge Philosophical Society
34. Examining rates and patterns of nucleotide substitution in plants
    Spencer V. Muse · 2000 · Plant Molecular Biology
35. Hierarchical Phylogenetic Models for Analyzing Multipartite Sequence Data
    Marc A. Suchard, Christina M. Ramirez, Janet S. Sinsheimer, Robert E. Weiss · 2003 · Systematic Biology
36. A Likelihood-Ratio Test of Monophyly
    John P. Huelsenbeck, David M. Hillis, Rasmus Nielsen · 1996 · Systematic Biology
37. Exploring Among-Site Rate Variation Models in a Maximum Likelihood Framework Using Empirical Data: Effects of Model Assumptions on Estimates of Topology, Branch Lengths, and Bootstrap Support
    Thomas R. Buckley, Chris Simon, Geoffrey Keith Chambers · 2001 · Systematic Biology
38. Reconstructing the phylogenetic relationships of the earth’s most diverse clade of freshwater fishes—order Cypriniformes (Actinopterygii: Ostariophysi): A case study using multiple nuclear loci and the mitochondrial genome
    Richard L. Mayden, Wei‐Jen Chen, HENRY L. JR. BART, Michael H. Doosey, Andrew M. Simons, Kevin L. Tang, Robert M. Wood, Mary K. Agnew, Lei Yang, M. Vincent Hirt et al. · 2008 · Molecular Phylogenetics and Evolution
39. Hidden Likelihood Support in Genomic Data: Can Forty-Five Wrongs Make a Right?
    John Gatesy, Richard H. Baker · 2005 · Systematic Biology
40. Rapid Global Spread of wRi-like Wolbachia across Multiple Drosophila
    Michael Turelli, Brandon S. Cooper, Kelly M. Richardson, Paul Ginsberg, Brooke Peckenpaugh, Chenling X. Antelope, Kevin J. Kim, Michael R. May, Antoine Abrieux, Derek A. Wilson et al. · 2018 · Current Biology
41. Testing the Cambrian explosion hypothesis by using a molecular dating technique
    Bromham, Lindell, Rambaut, Andrew, Fortey, Richard, Cooper, Alan, Penny, David · 1998 · Proceedings of the National Academy of Sciences
42. Selecting Models of Nucleotide Substitution: An Application to Human Immunodeficiency Virus 1 (HIV-1)
    David Posada, Keith A. Crandall · 2001 · Molecular Biology and Evolution
43. Does Choice in Model Selection Affect Maximum Likelihood Analysis?
    Jennifer Ripplinger, Jack M. Sullivan · 2008 · Systematic Biology
44. Jumping spider phylogeny (Araneae : Salticidae)
    Wayne P. Maddison, Marshal C. Hedin · 2003 · Invertebrate Systematics
45. Tree disagreement: Measuring and testing incongruence in phylogenies
    Paul Joseph Planet · 2005 · Journal of Biomedical Informatics
46. High genetic divergences indicate ancient separation of parthenogenetic lineages of the oribatid mite Platynothrus peltifer (Acari, Oribatida)
    Michael Heethoff, Katja Domes, Michael Laumann, Mark Maraun, Roy A. Norton, Stefan Scheu · 2006 · Journal of Evolutionary Biology
47. Sympatric speciation through intraspecific social parasitism
    Riitta Savolainen, Kari Vepsäläinen · 2003 · Proceedings of the National Academy of Sciences
48. The phylogenetic relationships among non-diplomystid catfishes as inferred from mitochondrial cytochrome b sequences; the search for the ictalurid sister taxon (Otophysi: Siluriformes)
    Michael Hardman · 2005 · Molecular Phylogenetics and Evolution
49. Macroevolutionary inferences from primate phylogeny
    Andy Purvis, Sean Nee, Paul Harvey · 1995 · Proceedings of the Royal Society B Biological Sciences
50. Recent Diversification Rates in North American Tiger Beetles Estimated from a Dated mtDNA Phylogenetic Tree
    Timothy G. Barraclough, Alfried P. Vogler · 2002 · Molecular Biology and Evolution
51. Statistical Tests of Gamma-Distributed Rate Heterogeneity in Models of Sequence Evolution in Phylogenetics
    Nick Goldman, Simon Whelan · 2000 · Molecular Biology and Evolution
52. Multiple Maxima of Likelihood in Phylogenetic Trees: An Analytic Approach
    Benny Chor, Michael D. Hendy, Barbara R. Holland, David Penny · 2000 · Molecular Biology and Evolution
53. Estimating Rate and Time in Molecular Phylogenies: Beyond the Molecular Clock?
    Michael J. Sanderson · 1998 · Springer eBooks
54. Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs
    Julien Yann Dutheil, Bastien Boussau · 2008 · BMC Evolutionary Biology
55. Iron Hydrogenases and the Evolution of Anaerobic Eukaryotes
    David Stephen Horner, Peter Gordon Foster, T. Martin Embley · 2000 · Molecular Biology and Evolution
56. Evolutionary analyses of DNA sequences subject to constraints of secondary structure.
    Spencer V. Muse · 1995 · Genetics
57. Distributions of Statistics Used for the Comparison of Models of Sequence Evolution in Phylogenetics
    Simon Whelan, Nick Goldman · 1999 · Molecular Biology and Evolution
58. Simple diagnostic statistical tests of models for DNA substitution
    Nick Goldman · 1993 · Journal of Molecular Evolution
59. Phylogeny of Salmonine Fishes Based on Growth Hormone Introns: Atlantic (Salmo) and Pacific (Oncorhynchus) Salmon Are Not Sister Taxa
    Todd H. Oakley, Ruth Brosi Phillips · 1999 · Molecular Phylogenetics and Evolution
60. Are any primroses (Primula) primitively monomorphic?
    Austin Mast, Sylvia Kelso, Elena Conti · 2006 · New Phytologist
61. Reconstruction of ancestral protein sequences and its applications
    Wei Cai, Jimin Pei, Nick V. Grishin · 2004 · BMC Evolutionary Biology
62. Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap
    Kurt R. Wollenberg, William R. Atchley · 2000 · Proceedings of the National Academy of Sciences
63. Pleistocene Speciation and the Mitochondrial DNA Clock
    Brian S. Arbogast, Joseph B. Slowinski · 1998 · Science
64. A Partitioned Likelihood Analysis of Swallowtail Butterfly Phylogeny (Lepidoptera: Papilionidae)
    Michael S. Caterino, Robert D. Reed, May M. Kuo, Felix A. H. Sperling · 2001 · Systematic Biology
65. Patterns of morphologic diversification among the Rostroconchia
    Peter J. Wagner · 1997 · Paleobiology
66. Recreating ancestral proteins
    Belinda S. W. Chang, Michael J. Donoghue · 2000 · Trends in Ecology & Evolution
67. Using Phylogenies to Test Macroevolutionary Hypotheses of Trait Evolution in Cranes (Gruinae)
    Arne Ø. Mooers, Steven M. Vamosi, Dolph Schluter · 1999 · The American Naturalist
68. Statistical alignment: computational properties, homology testing and goodness-of-fit 1 1Edited by J. Karn
    Jotun Hein, Carsten Wiuf, Bjarne Knudsen, Michael Möller, G. Wibling · 2000 · Journal of Molecular Biology
69. One species or at least eight? Delimitation and distribution of Frullania tamarisci (L.) Dumort. s. l. (Jungermanniopsida, Porellales) inferred from nuclear and chloroplast DNA markers
    Jochen Heinrichs, Jörn Hentschel, Andrea Bombosch, Anja Fiebig, Judith Reise, Michel Edelmann, Hans‐Peter Kreier, Alfons Schäfer‐Verwimp, Steffen Caspari, Alexander R. Schmidt et al. · 2010 · Molecular Phylogenetics and Evolution
70. Molecular Evolutionary Genetics Analysis
    Koichiro Tamura, Joel T. Dudley, Masatoshi Nei, Sudhir Kumar · 2007
71. The Effects of Nucleotide Substitution Model Assumptions on Estimates of Nonparametric Bootstrap Support
    Thomas R. Buckley, Cliff Cunningham · 2002 · Molecular Biology and Evolution
72. STATISTICAL TESTS OF HOST-PARASITE COSPECIATION
    John P. Huelsenbeck, Bruce H. Rannala, Ziheng Yang · 1997 · Evolution
73. Comparative phylogeography of woodland reptiles in California: repeated patterns of cladogenesis and population expansion
    Chris R. Feldman, Greg S. Spicer · 2006 · Molecular Ecology
74. Nuclear and Nucleomorph SSU rDNA Phylogeny in the Cryptophyta and the Evolution of Cryptophyte Diversity
    Kerstin Hoef‐Emden, Birger Marin, Michael Melkonian · 2002 · Journal of Molecular Evolution
75. Phylogeny and biogeography of Rhododendron subsection Pontica, a group with a tertiary relict distribution
    Richard I. Milne · 2004 · Molecular Phylogenetics and Evolution
76. Phylogeny and Biogeography of the Flowering Plant Genus Styrax (Styracaceae) Based on Chloroplast DNA Restriction Sites and DNA Sequences of the Internal Transcribed Spacer Region
    Peter W. Fritsch · 2001 · Molecular Phylogenetics and Evolution
77. Variation in Evolutionary Processes at Different Codon Positions
    Lee Bofkin, Nick Goldman · 2006 · Molecular Biology and Evolution
78. Quaternary history and contemporary patterns in a currently expanding species
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79. CONTRASTING QUATERNARY HISTORIES IN AN ECOLOGICALLY DIVERGENT SISTER PAIR OF LOW-DISPERSING INTERTIDAL FISH (XIPHISTER) REVEALED BY MULTILOCUS DNA ANALYSIS
    Michael J. Hickerson, Cliff Cunningham · 2005 · Evolution
80. Phylogeny and biogeography of Chinese sisorid catfishes re-examined using mitochondrial cytochrome b and 16S rRNA gene sequences
    Xianguang Guo, Shunping He, Yaoguang Zhang · 2005 · Molecular Phylogenetics and Evolution
81. AliSim: A Fast and Versatile Phylogenetic Sequence Simulator for the Genomic Era
    Nhan Ly-Trong, Suha Naser-Khdour, Robert Lanfear, Bùi Quang Minh · 2022 · Molecular Biology and Evolution
82. A Maximum-Likelihood Analysis of Eight Phylogenetic Markers in Gallwasps (Hymenoptera: Cynipidae): Implications for Insect Phylogenetic Studies
    Antonis Rokas, Johan A. A. Nylander, Fredrik Ronquist, Graham N. Stone · 2002 · Molecular Phylogenetics and Evolution
83. Repeat intercontinental dispersal and Pleistocene speciation in disjunct Mediterranean and desert Senecio (Asteraceae)
    Max Coleman, Aaron Liston, Joachim W. Kadereit, Richard J. Abbott · 2003 · American Journal of Botany
84. Molecular systematics of the South American caviomorph rodents: relationships among species and genera in the family Octodontidae
    Rodney L. Honeycutt, Diane L. Rowe, Milton H. Gallardo · 2003 · Molecular Phylogenetics and Evolution
85. Molecular phylogeny of the Bacidiaceae (Lecanorales, lichenized Ascomycota)
    Stefan Ekman · 2001 · Mycological Research
86. Accounting for coalescent stochasticity in testing phylogeographical hypotheses: modelling Pleistocene population structure in the Idaho giant salamanderDicamptodon aterrimus
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87. Patterns of Speciation Inferred from Mitochondrial DNA in North American Chthamalus (Cirripedia: Balanomorpha: Chthamaloidea)
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88. Interspecific relationships and origins of Taxaceae and Cephalotaxaceae revealed by partitioned Bayesian analyses of chloroplast and nuclear DNA sequences
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89. Testing Nested Phylogenetic and Phylogeographic Hypotheses in the Plethodon vandykei Species Group
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90. Systematics of the Lizard Family Pygopodidae with Implications for the Diversification of Australian Temperate Biotas
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91. THE DYNAMICS OF NATURAL SELECTION AND VICARIANCE IN THE DOMINICAN ANOLE: PATTERNS OF WITHIN-ISLAND MOLECULAR AND MORPHOLOGICAL DIVERGENCE
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92. Reconstructing Ancestral Patterns of Colonization and Dispersal in the Hawaiian Understory Tree Genus Psychotria (Rubiaceae): A Comparison of Parsimony and Likelihood Approaches
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93. Molecular systematics of the Cyprinoidea (Teleostei: Cypriniformes), the world’s largest clade of freshwater fishes: Further evidence from six nuclear genes
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94. A smaller Macadamia from a more vagile tribe: inference of phylogenetic relationships, divergence times, and diaspore evolution in Macadamia and relatives (tribe Macadamieae; Proteaceae)
    Austin Mast, Crystal L. Willis, Eric H. Jones, Katherine M. Downs, Peter H. Weston · 2008 · American Journal of Botany
95. Historical biogeography and the origin of stomatal distributions in Banksia and Dryandra (Proteaceae) based on their cpDNA phylogeny
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96. The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets
    Xiaodong Jiang, Scott V. Edwards, Liang Liu · 2020 · Systematic Biology
97. Phylogeny and Biogeography of the Arbutoideae (Ericaceae): Implications for the Madrean-Tethyan Hypothesis
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98. A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa
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99. Biogeographic history of an Australian freshwater shrimp, Paratya australiensis (Atyidae): the role life history transition in phylogeographic diversification
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100. Molecular Phylogenetics of Emydine Turtles: Taxonomic Revision and the Evolution of Shell Kinesis
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