Statistical tests of models of DNA substitution

Cited by (736)

Items 201–300 of 736

1. Under-parameterized Model of Sequence Evolution Leads to Bias in the Estimation of Diversification Rates from Molecular Phylogenies
   Liam J. Revell, Luke J. Harmon, Richard E. Glor · 2005 · Systematic Biology
2. The Leishmania donovani complex: Genotypes of five metabolic enzymes (ICD, ME, MPI, G6PDH, and FH), new targets for multilocus sequence typing
   Eva Zemanová, Milan Jirků, Isabel Larguinho Maurício, Aleš Horák, Michael A. Miles, Julius Lukeš · 2006 · International Journal for Parasitology
3. Evaluating Hypotheses on the Origin and Evolution of the New Zealand Alpine Cicadas (Maoricicada) Using Multiple-Comparison Tests of Tree Topology
   Thomas R. Buckley, Chris Simon, Hidetoshi Shimodaira, Geoffrey Keith Chambers · 2001 · Molecular Biology and Evolution
4. Likelihood Analysis of Phylogenetic Networks Using Directed Graphical Models
   Korbinian Strimmer, Vincent Moulton · 2000 · Molecular Biology and Evolution
5. The effect of habitat type on speciation rates and range movements in aquatic beetles: inferences from species‐level phylogenies
   Ignacio Ribera, Timothy G. Barraclough, Alfried P. Vogler · 2001 · Molecular Ecology
6. Patterns of Nucleotide Substitution in Mitochondrial Protein Coding Genes of Vertebrates
   Sudhir Kumar · 1996 · Genetics
7. Improved dating of the human/chimpanzee separation in the mitochondrial DNA tree: Heterogeneity among amino acid sites
   Adachi, Jun, Hasegawa, Masami · 1995 · Journal of Molecular Evolution
8. Molecular phylogeny of two lineages of Leuciscinae cyprinids (Telestes and Scardinius) from the peri-Mediterranean area based on cytochrome b data
   Valerio Ketmaier, Pier Giorgio Bianco, Marina Cobolli, Marijana Krivokapić, Romolo Caniglia, Elvira De Matthaeis · 2004 · Molecular Phylogenetics and Evolution
9. Cryptic speciation and patterns of phenotypic variation of a highly variable acanthocephalan parasite
   Michelle L. Steinauer, Brent B. Nickol, Guillermo Ortı́ · 2007 · Molecular Ecology
10. Phylogenetic systematics of Southeast Asian flying lizards (Iguania: Agamidae Draco) as inferred from mitochondrial DNA sequence data
    Jimmy A. McGuire, Kiew Bong Heang · 2001 · Biological Journal of the Linnean Society
11. On the Consistency of Maximum Likelihood Estimation of Phylogenetic Trees from Nucleotide Sequences
    James S. Rogers · 1997 · Systematic Biology
12. Phylogeny, Genome Evolution, and Host Specificity of Single-Stranded RNA Bacteriophage (Family Leviviridae)
    Jonathan P. Bollback, John P. Huelsenbeck · 2001 · Journal of Molecular Evolution
13. A Molecular Phylogenetic Study of the Palmae (Arecaceae) Based on atpB, rbcL, and 18S nrDNA Sequences
    William James Hahn · 2002 · Systematic Biology
14. THE PHYLOGENETIC RELATIONSHIP OF PFIESTERIA PISCICIDA, CRYPTOPERIDINIOPSOID SP. AMYLOODINOUM OCELLATUM AND A PFIESTERIA‐LIKE DINOFLAGELLATE TO OTHER DINOFLAGELLATES AND APICOMPLEXANS
    Richard Wayne Litaker, Patricia Ann Tester, A. Colorni, Michael G. Levy, Edward J. Noga · 1999 · Journal of Phycology
15. Genetic evidence of cryptic speciation within hammerhead sharks (Genus Sphyrna)
    Joseph M. Quattro, Douglas S. Stoner, William B. Driggers, Clifford Anderson, K. A. Priede, E. C. Hoppmann, Nathan H. Campbell, Kanesa Duncan, James M. Grady · 2005 · Marine Biology
16. Comparative Performance of Bayesian and AIC-Based Measures of Phylogenetic Model Uncertainty
    Michael E. Alfaro, John P. Huelsenbeck · 2006 · Systematic Biology
17. Why Do Paralogs Persist? Molecular Evolution of CYCLOIDEA and Related Floral Symmetry Genes in Antirrhineae (Veronicaceae)
    Lena C. Hileman · 2003 · Molecular Biology and Evolution
18. Biogeography and phylogeny of the New Zealand cicada genera (Hemiptera: Cicadidae) based on nuclear and mitochondrial DNA data
    Peter Arensburger, Thomas R. Buckley, Chris Simon, Maxwell S. Moulds, Kent E. Holsinger · 2004 · Journal of Biogeography
19. Molecular insights into the phylogeny and subgeneric classification of Frullania Raddi (Frullaniaceae, Porellales)
    Jörn Hentschel, Matthew J. von Konrat, Tamás Pócs, Alfons Schäfer‐Verwimp, A. Jonathan Shaw, Harald Schneider, Jochen Heinrichs · 2009 · Molecular Phylogenetics and Evolution
20. Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes
    Daniel Barker, Andrew Meade, Mark D. Pagel · 2006 · Bioinformatics
21. Stochastic Search Strategy for Estimation of Maximum Likelihood Phylogenetic Trees
    Laura A. Salter, Dennis K. Pearl · 2001 · Systematic Biology
22. Poor Fit to the Multispecies Coalescent is Widely Detectable in Empirical Data
    Noah M. Reid, Sarah M. Hird, Jeremy M. Brown, Tara A. Pelletier, John D. McVay, Jordan D. Satler, Bryan C. Carstens · 2013 · Systematic Biology
23. Identification of domestic cattle hybrids in wild cattle and bison species: a general approach using mtDNA markers and the parametric bootstrap
    Todd J. Ward, Joseph P. Bielawski, Scott K. Davis, Joe W. Templeton, James N. Derr · 1999 · Animal Conservation
24. Molecular Systematics and Biogeography of the Fanged Frogs of Southeast Asia
    Sharon B. Emerson, Robert F. Inger, Djoko Tjahjono Iskandar · 2000 · Molecular Phylogenetics and Evolution
25. Is Character Weighting a Panacea for the Problem of Data Heterogeneity in Phylogenetic Analysis?
    John P. Huelsenbeck, David L. Swofford, Cliff Cunningham, James J. Bull, Peter J. Waddell · 1994 · Systematic Biology
26. Can We Identify Genes with Increased Phylogenetic Reliability?
    Vinson Patrick Doyle, Randee E. Young, Gavin J. P. Naylor, Jeremy M. Brown · 2015 · Systematic Biology
27. Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods
    Nicholas A. Bokulich, Michał Ziemski, Michael Scott Robeson, Benjamin D. Kaehler · 2020 · Computational and Structural Biotechnology Journal
28. Mutation Patterns of Mitochondrial H- and L-Strand DNA in Closely Related Cyprinid Fishes
    Joseph P. Bielawski, John R. Gold · 2002 · Genetics
29. Phylogenetic Relationships among Bullhead Catfishes of the Genus Ameiurus (Siluriformes: Ictaluridae)
    Michael Hardman, Lawrence M. Page · 2003 · Copeia
30. Estimating the Frequency of Events That Cause Multiple-Nucleotide Changes
    Simon Whelan, Nick Goldman · 2004 · Genetics
31. Phylogenetic Characterization and Molecular Evolution of Bacterial Endosymbionts in Psyllids (Hemiptera: Sternorrhyncha)
    Allen Spaulding, Carol D. von Dohlen · 1998 · Molecular Biology and Evolution
32. Phylogenetic Origins of the Himalayan Endemic Dolomiaea , Diplazoptilon and Xanthopappus (Asteraceae: Cardueae) Based on Three DNA Regions
    Yujin Wang, Jianquan Liu, Georg Miehe · 2007 · Annals of Botany
33. Understanding the molecular epidemiology of foot-and-mouth-disease virus
    Joern Klein · 2008 · Infection Genetics and Evolution
34. Ribosomal DNA in the GrasshopperPodisma pedestris: Escape From Concerted Evolution
    Irene Keller, Ioana Cristina Chintauan-Marquier, Paris Veltsos, Richard A. Nichols · 2006 · Genetics
35. The Comb Jelly Opsins and the Origins of Animal Phototransduction
    Feuda, Roberto, Rota-Stabelli, Omar, Oakley, Todd H., Pisani, Davide · 2014 · Genome Biology and Evolution
36. Molecular Evolution of the Wingless Gene and Its Implications for the Phylogenetic Placement of the Butterfly Family Riodinidae (Lepidoptera: Papilionoidea)
    Dana L. Campbell, Andrew V. Z. Brower, Naomi E. Pierce · 2000 · Molecular Biology and Evolution
37. Phylogeny and Biogeography of Cercis (Fabaceae): Evidence from Nuclear Ribosomal ITS and Chloroplast ndhF Sequence Data
    Charles “Chuck” Davis, Peter W. Fritsch, Jianhua Li, Michael J. Donoghue · 2002 · BioOne Complete (BioOne)
38. Molecular evolution of the hepatitis B virus genome
    Ziheng Yang, Ian James Lauder, Hsiang Ju Lin · 1995 · Journal of Molecular Evolution
39. Maximum likelihood with multiparameter models of substitution
    Elisabeth Ren�e, Elisabeth R.M. Tillier · 1994 · Journal of Molecular Evolution
40. Maximum likelihood estimation of phylogeny using stratigraphic data
    John P. Huelsenbeck, Bruce H. Rannala · 1997 · Paleobiology
41. Empirical Problems of the Hierarchical Likelihood Ratio Test for Model Selection
    Diego Pol · 2004 · Systematic Biology
42. Using models of nucleotide evolution to build phylogenetic trees
    David H. Bos, David Posada · 2004 · Developmental & Comparative Immunology
43. Molecular phylogeny and biogeography of Oriental voles: genus Eothenomys (Muridae, Mammalia)
    Jing Luo, Dong-ming Yang, Hitoshi Suzuki, Yingxiang Wang, Wei‐Jen Chen, Kevin L. Campbell, Ya‐Ping Zhang · 2004 · Molecular Phylogenetics and Evolution
44. Phylogenetic Signal and its Decay in Mitochondrial SSU and LSU rRNA Gene Fragments of Anisoptera
    Bernhard Y. Misof, Andreas Rickert, Thomas R. Buckley, Günther Fleck, Klaus Peter Sauer · 2001 · Molecular Biology and Evolution
45. THE LIKELIHOOD NODE DENSITY EFFECT AND CONSEQUENCES FOR EVOLUTIONARY STUDIES OF MOLECULAR RATES
    Andrew F. Hugall, Michael S. Y. Lee · 2007 · Evolution
46. Molecular systematics: A synthesis of the common methods and the state of knowledge
    Diego San Mauro, Ainhoa Agorreta · 2010 · Cellular & Molecular Biology Letters
47. Variation Across Mitochondrial Gene Trees Provides Evidence for Systematic Error: How Much Gene Tree Variation Is Biological?
    Emilie J. Richards, Jeremy M. Brown, Anthony J. Barley, Rebecca A. Chong, Robert C. Thomson · 2018 · Systematic Biology
48. A phylogenetic analysis of the Arecoid Line of palms based on plastid DNA sequence data
    William James Hahn · 2002 · Molecular Phylogenetics and Evolution
49. Quartet-Mapping, a Generalization of the Likelihood-Mapping Procedure
    Kay Nieselt, Arndt von Haeseler · 2001 · Molecular Biology and Evolution
50. Exploring population genetic structure in three species of Lesser Antillean bats
    Bryan C. Carstens, Jack M. Sullivan, Liliana M. Dávalos, Peter A. Larsen, Scott C. Pedersen · 2004 · Molecular Ecology
51. DIVERSIFICATION OF SULAWESI MACAQUE MONKEYS: DECOUPLED EVOLUTION OF MITOCHONDRIAL AND AUTOSOMAL DNA
    Ben J. Evans, Jatna Supriatna, Noviar Andayani, Don J. Melnick · 2003 · Evolution
52. PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment
    Botond Sipos, Tim Massingham, Gregory E. Jordan, Nick Goldman · 2011 · BMC Bioinformatics
53. The Pleistocene glaciations and the evolutionary history of the polytypic snail species Arianta arbustorum (Gastropoda, Pulmonata, Helicidae)
    Edmund Gittenberger, William H. Piel, Dick S. J. Groenenberg · 2003 · Molecular Phylogenetics and Evolution
54. Relationships among four genera of mojarras (Teleostei: Perciformes: Gerreidae) from the western Atlantic and their tentative placement among percomorph fishes
    Wei‐Jen Chen, Ramon Ruiz-Carus, Guillermo Ortı́ · 2007 · Journal of Fish Biology
55. Stochastic Search Strategy for Estimation of Maximum Likelihood Phylogenetic Trees
    Laura A. Salter, Dennis K. Pearl · 2001 · Systematic Biology
56. Molecular systematics of five Onchocerca species (Nematoda: Filarioidea) including the human parasite, O. volvulus, suggest sympatric speciation
    Ramiro Morales‐Hojas, Robert Cheke, R.J. Post · 2006 · Journal of Helminthology
57. Philosophy and Phylogenetic Inference: A Comparison of Likelihood and Parsimony Methods in the Context of Karl Popper's Writings on Corroboration
    Kevin de Queiroz, Steven Poe · 2001 · Systematic Biology
58. Neotropical roots of a Polynesian spice: the hybrid origin of Tahitian vanilla, Vanilla tahitensis (Orchidaceae)
    Pesach Lubinsky, Kenneth M. Cameron, María del Carmen Molina, Maurice Wong, Sandra Lepers‐Andrzejewski, Arturo Gómez‐Pompa, Seung‐Chul Kim · 2008 · American Journal of Botany
59. 28S rDNA Evolution in the Eumalacostraca and the Phylogenetic Position of Krill
    Simon Jarman, Stephen Nicol, Nicholas G. Elliott, Andrew McMinn · 2000 · Molecular Phylogenetics and Evolution
60. Phylogenetic Model Evaluation
    Lars Sommer Jermiin, Vivek Jayaswal, Faisal M. Ababneh, John Robinson · 2008 · Methods in molecular biology
61. Mitochondrial DNA Diversity and Population Structure among Southern Right Whales (Eubalaena australis)
    Nathalie J. Patenaude, Vicky A. Portway, Catherine M. Schaeff, John L. Bannister, Peter B. Best, Roger S. Payne, Vicky Rowntree, Mariana Rivarola, C. Scott Baker · 2007 · Journal of Heredity
62. Divergence Times and Historical Biogeography of Nymphaeales
    Mi‐Jeong Yoo, Charles D. Bell, Pamela S. Soltis, Pamela S. Soltis · 2005 · Systematic Botany
63. 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
64. Molecular markers: progress and prospects for understanding reproductive ecology in elasmobranchs
    David S. Portnoy, Edward J. Heist · 2012 · Journal of Fish Biology
65. A Phylogeny of the Damselfly Genus Calopteryx (Odonata) Using Mitochondrial 16S rDNA Markers
    Bernhard Y. Misof, Cort L. Anderson, Heike Hadrys · 2000 · Molecular Phylogenetics and Evolution
66. Molecular Polytomies
    Joseph B. Slowinski · 2001 · Molecular Phylogenetics and Evolution
67. Probabilistic models of DNA sequence evolution with context dependent rates of substitution
    Jens Ledet Jensen, Anne-Mette Krabbe Pedersen · 2000 · Advances in Applied Probability
68. A Phylogenomic Approach to Resolve the Basal Pterygote Divergence
    Sabrina Simon, S. Strauss, Arndt von Haeseler, Heike Hadrys · 2009 · Molecular Biology and Evolution
69. A Practical Guide to Design and Assess a Phylogenomic Study
    Jesús Lozano-Fernández · 2022 · Genome Biology and Evolution
70. The phylogenetic utility of nucleotide sequences of sorbitol 6‐phosphate dehydrogenase in Prunus (Rosaceae)
    Esteban Bortiri, Sang‐Hun Oh, Fangyou Gao, Daniel Potter · 2002 · American Journal of Botany
71. Molecular phylogenetic evidence for multiple gains or losses of ant mutualism within the aphid genus Chaitophorus
    Alexander W. Shingleton, David L. Stern · 2002 · Molecular Phylogenetics and Evolution
72. DO PHYLOGENETIC METHODS PRODUCE TREES WITH BIASED SHAPES?
    John P. Huelsenbeck, Mark Kirkpatrick · 1996 · Evolution
73. Steady Plio-Pleistocene diversification and a 2-million-year sympatry threshold in a New Zealand cicada radiation
    David C. Marshall, Karen Slon, John R. Cooley, Kathy B. R. Hill, Chris Simon · 2008 · Molecular Phylogenetics and Evolution
74. A phylogenetic analysis of woodpeckers and their allies using 12S, Cyt b, and COI nucleotide sequences (class Aves; order Piciformes)
    David Webb, William S. Moore · 2005 · Molecular Phylogenetics and Evolution
75. Tadpoles Balance Foraging and Predator Avoidance: Effects of Predation, Pond Drying, and Hunger
    Christine M. Bridges · 2002 · Journal of Herpetology
76. Molecular Phylogeny of the Drosophila virilis Species Group (Diptera: Drosophilidae) Inferred from Mitochondrial 12S and 16S Ribosomal RNA Genes
    Greg S. Spicer, Charles D. Bell · 2002 · Annals of the Entomological Society of America
77. Clustering Genes of Common Evolutionary History
    Kevin C. Gori, Tomasz Suchan, Nadir Álvarez, Nick Goldman, Christophe Dessimoz · 2016 · Molecular Biology and Evolution
78. Performance of likelihood ratio tests of evolutionary hypotheses under inadequate substitution models
    J. Zhang · 1999 · Molecular Biology and Evolution
79. Molecular phylogeny and historical biogeography of the land snail genus Solatopupa (Pulmonata) in the peri-Tyrrhenian area
    Valerio Ketmaier, Folco Giusti, Adalgisa Caccone · 2006 · Molecular Phylogenetics and Evolution
80. Phylogenetic analyses and the fossil record: Tests and inferences, hypotheses and models
    Peter J. Wagner · 2000 · Paleobiology
81. Complexity of the Likelihood Surface for a Large DNA Dataset
    Laura A. Salter · 2001 · Systematic Biology
82. Short‐faced bats (Phyllostomidae: Stenodermatina): a Caribbean radiation of strict frugivores
    Liliana M. Dávalos · 2006 · Journal of Biogeography
83. A Test of a Mitochondrial Gene-Based Phylogeny of Woodpeckers (Genus Picoides) Using an Independent Nuclear Gene, β-Fibrinogen Intron 7
    Amy C. Weibel, William S. Moore · 2002 · Molecular Phylogenetics and Evolution
84. Selecting models of evolution
    David Posada · 2009 · Cambridge University Press eBooks
85. Biogeography of Nymphaeales: extant patterns and historical events
    Cornelia Löhne, Mi‐Jeong Yoo, Thomas Borsch, John H. Wiersema, Volker Wilde, Charles D. Bell, Wilhelm Barthlott, Pamela S. Soltis, Pamela S. Soltis · 2008 · Taxon
86. Maximum‐Likelihood Analysis Using TREE ‐ PUZZLE
    Heiko A. Schmidt, Arndt von Haeseler · 2003 · Current Protocols in Bioinformatics
87. Phylogeny of Habronattus jumping spiders (Araneae: Salticidae), with consideration of genital and courtship evolution
    Wayne P. Maddison, Marshal C. Hedin · 2003 · Systematic Entomology
88. Extensive mtDNA variation within the yellow-pine chipmunk, Tamias amoenus (Rodentia: Sciuridae), and phylogeographic inferences for northwest North America
    John R. Demboski, Jack M. Sullivan · 2003 · Molecular Phylogenetics and Evolution
89. Biogeography of Asterias: North Atlantic Climate Change and Speciation
    John P. Wares · 2001 · Biological Bulletin
90. The Two AGPase Subunits Evolve at Different Rates in Angiosperms, yet They Are Equally Sensitive to Activity-Altering Amino Acid Changes When Expressed in Bacteria
    Nikolaos Georgelis, Edward Louis Braun, Janine R. Shaw, L. Curtis Hannah · 2007 · The Plant Cell
91. Molecular phylogenetics of myliobatiform fishes (Chondrichthyes: Myliobatiformes), with comments on the effects of missing data on parsimony and likelihood
    Katherine A. Dunn, John D. McEachran, Rodney L. Honeycutt · 2003 · Molecular Phylogenetics and Evolution
92. Clade support measures and their adequacy
    Taran Grant, Arnold G. Kluge · 2008 · Cladistics
93. Inferring Complex DNA Substitution Processes on Phylogenies Using Uniformization and Data Augmentation
    Ligia Monica Mateiu, Bruce H. Rannala · 2006 · Systematic Biology
94. Genetic diversity analyses of grapevine Rupestris stem pitting-associated virus reveal distinct population structures in scion versus rootstock varieties
    Baozhong Meng, Ana Rita Rebelo, Helen Fisher · 2006 · Journal of General Virology
95. Integration of morphological and molecular data sets in estimating fungal phytogenies
    Francois M. Lutzoni, Rytas J. Vilgalys · 1995 · Canadian Journal of Botany
96. Molecular phylogenetic relationships in the aquatic snail genus Lymnaea , the intermediate host of the causative agent of fascioliasis: insights from broader taxon sampling
    ELPIDO A. REMIGIO · 2002 · Parasitology Research
97. The evolutionary origin of Indian Ocean tortoises (Dipsochelys)
    Eric P. Palkovacs, Justin Gerlach, Adalgisa Caccone · 2002 · Molecular Phylogenetics and Evolution
98. Evaluating Model Performance in Evolutionary Biology
    Jeremy M. Brown, Robert C. Thomson · 2018 · Annual Review of Ecology Evolution and Systematics
99. The “Naked Coral” Hypothesis Revisited – Evidence for and Against Scleractinian Monophyly
    Marcelo Visentini Kitahara, Mei‐Fang Lin, Sylvain Forêt, Gavin A. Huttley, David John Miller, Chaolun Allen Chen · 2014 · PLoS ONE
100. Tramps, narrow endemics and morphologically cryptic species in the epiphyllous liverwort Diplasiolejeunea
     Shanshan Dong, Alfons Schäfer‐Verwimp, Philipp Meinecke, Kathrin Feldberg, Andrea Bombosch, Tamás Pócs, Alexander R. Schmidt, Joachim Reitner A, Harald Schneider, Jochen Heinrichs · 2012 · Molecular Phylogenetics and Evolution