Statistical tests of models of DNA substitution

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Items 301–400 of 736

1. Quaternary palaeoenvironmental oscillations drove the evolution of the EurasianCarassius auratuscomplex (Cypriniformes, Cyprinidae)
   Yun Gao, Shuyan Wang, Jing Luo, Robert W. Murphy, Rui Du, Shi‐Fang Wu, Zhu Chun-ling, Yan Li, Andrei D. Poyarkov, Sang Ngoc Nguyen et al. · 2012 · Journal of Biogeography
2. PHYLOGENETIC RELATIONSHIPS AMONG THE SPECIES OF AEGLA (ANOMURA: AEGLIDAE) FRESHWATER CRABS FROM CHILE
   Marcos Pérez‐Losada, Keith A Crandall, Carlos G. Jara, Georginam Bond-Buckup · 2002 · Journal of Crustacean Biology
3. Phylogeographic analysis of the Bufo gargarizans species complex: A revisit
   Jinzhong Fu, Cameron J. Weadick, Xiaomao Zeng, Yuezhao Wang, Zhijun Liu, Yuchi Zheng, Cheng Li, Ying Hu · 2005 · Molecular Phylogenetics and Evolution
4. Phylogenetic evidence for a single long-lived clade of crustacean cyclic parthenogens and its implications for the evolution of sex
   Derek J. Taylor, Teresa J. Crease, Wesley M. Brown · 1999 · Proceedings of the Royal Society B Biological Sciences
5. Modeling nucleotide evolution: A heterogeneous rate analysis
   Colleen Kelly, John Rice · 1996 · Mathematical Biosciences
6. Molecular Phylogeny of a Cosmopolitan Group of Woodpeckers (Genus Picoides) Based on COI and cyt b Mitochondrial Gene Sequences
   Amy C. Weibel, William S. Moore · 2002 · Molecular Phylogenetics and Evolution
7. Historical biogeography and speciation in the Neotropical highlands: Molecular phylogenetics of the jay genus Cyanolyca
   Elisa Bonaccorso · 2008 · Molecular Phylogenetics and Evolution
8. Molecular Evolution of FLORICAULA/LEAFY Orthologs in the Andropogoneae (Poaceae)
   Kirsten Bomblies, John Doebley · 2005 · Molecular Biology and Evolution
9. Phylogenetic relationships of four species of floating gobies (Gymnogobius) as inferred from partial mitochondrial cytochrome b gene sequences
   Shigeo Harada, Sang-Rin Jeon, Izumi Kinoshita, Masaru Tanaka, Mutsumi Nishida · 2002 · Ichthyological Research
10. Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data
    David Alejandro Duchêne, Niklas Mather, Cara Van Der Wal, Simon Y. W. Ho · 2021 · Systematic Biology
11. A phylogenetic analysis of the emberizid sparrows based on three mitochondrial genes
    Rebecca J. Carson, Greg S. Spicer · 2003 · Molecular Phylogenetics and Evolution
12. Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniformes): Evidence from the mitochondrial genome
    Shunping He, Xun Gu, Richard L. Mayden, Wei‐Jen Chen, Kevin W. Conway, Yiyu Chen · 2007 · Molecular Phylogenetics and Evolution
13. Chloroplast DNA phylogeny of the woody Sonchus alliance (Asteraceae: Sonchinae) in the Macaronesian Islands
    Chung-Hee Lee, Seung‐Chul Kim, Karen E. Lundy, Arnoldo Santos‐Guerra · 2005 · American Journal of Botany
14. Molecular systematics and patterns of morphological evolution in the Centropagidae (Copepoda: Calanoida) of Argentina
    Sarah J. Adamowicz, Silvina Menu-Marque, Paul D. N. Hebert, Andy Purvis · 2007 · Biological Journal of the Linnean Society
15. The Inference of Stepwise Changes in Substitution Rates Using Serial Sequence Samples
    Alexei J. Drummond, Roald Forsberg, Allen G. Rodrigo · 2001 · Molecular Biology and Evolution
16. Tempo and mode of recurrent polyploidization in the Carassius auratus species complex (Cypriniformes, Cyprinidae)
    Jun Luo, Yun Gao, W Ma, X-y Bi, S-y Wang, Jing Wang, Y-q Wang, Jing Chai, Rui Du, S-f Wu et al. · 2014 · Heredity
17. Identifying Conflicting Signal in a Multigene Analysis Reveals a Highly Resolved Tree: The Phylogeny of Rodentia (Mammalia)
    Ronald W. DeBry · 2003 · Systematic Biology
18. Visualizing Conflicting Evolutionary Hypotheses in Large Collections of Trees: Using Consensus Networks to Study the Origins of Placentals and Hexapods
    Barbara R. Holland, Frédéric Delsuc, Vincent Moulton · 2005 · Systematic Biology
19. Molecular Phylogenetics and Evolution of Maternal Care in Membracine Treehoppers
    Chung‐Ping Lin, Bryan N. Danforth, Thomas K. Wood · 2004 · Systematic Biology
20. ON THE PHYLOGENETIC POSITIONING OF THE SOUTH AMERICAN FRESHWATER CRAYFISH GENERA (DECAPODA: PARASTACIDAE)
    Keith A. Crandall, Ludwig Buckup, James W. Fetzner, Carlos G. Jara · 2000 · Journal of Crustacean Biology
21. Molecular phylogenetic analysis of Commiphora (Burseraceae) yields insight on the evolution and historical biogeography of an “impossible” genus
    Andrea Weeks, Beryl Brintnall Simpson · 2006 · Molecular Phylogenetics and Evolution
22. Evolution of the Inflated Calyx Syndrome in Solanaceae
    Jin‐Yong Hu, Heinz Saedler · 2007 · Molecular Biology and Evolution
23. Maximum Likelihood Methods for Detecting Adaptive Protein Evolution
    Joseph P. Bielawski, Ziheng Yang · 2005 · Statistics in the health sciences
24. Molecular Systematics of Old World Stripe-Necked Turtles (Testudines: Mauremys)
    Chris R. Feldman, James Ford Parham · 2004 · Biodiversity Heritage Library (Smithsonian Institution)
25. INTRASPECIFIC VARIATION AND GEOGRAPHIC ISOLATION IN IDOTEA BALTHICA (ISOPODA: VALVIFERA)
    John P. Wares · 2001 · Journal of Crustacean Biology
26. Extended phylogeny and a revised generic classification of thePannariaceae(Peltigerales, Ascomycota)
    Stefan Ekman, Mats Wedin, Louise Lindblom, P. M. Jørgensen · 2014 · The Lichenologist
27. Phylogenetic relationships, taxonomy, and morphological evolution in Dipsacaceae (Dipsacales) inferred by DNA sequence data
    Sara E. Carlson, Veronika E. Mayer, Michael J. Donoghue · 2009 · Taxon
28. Base Compositional Bias and Phylogenetic Analyses: A Test of the “Flying DNA” Hypothesis
    Ronald A. Van Den Bussche, Robert J. Baker, John P. Huelsenbeck, David M. Hillis · 1998 · Molecular Phylogenetics and Evolution
29. The Evolution of North American Elymus (Triticeae, Poaceae) Allotetraploids: Evidence from Phosphoenolpyruvate Carboxylase Gene Sequences
    D. Megan Helfgott, Roberta J. Mason‐Gamer · 2004 · Systematic Botany
30. ModelTeller: Model Selection for Optimal Phylogenetic Reconstruction Using Machine Learning
    Shiran Abadi, Oren Avram, Saharon Rosset, Tal Pupko, Itay Mayrose · 2020 · Molecular Biology and Evolution
31. Conflict and resolution between phylogenies inferred from molecular and phenotypic data sets for hagfish, lampreys, and gnathostomes
    Thomas J. Near · 2009 · Journal of Experimental Zoology Part B Molecular and Developmental Evolution
32. Rooting a phylogenetic tree with nonreversible substitution models.
    Yap, Von Bing, Speed, Terry · 2005 · BMC Evolutionary Biology
33. The devil in the details: interactions between the branch-length prior and likelihood model affect node support and branch lengths in the phylogeny of the Psoraceae
    Ekman, Stefan, Blaalid, Rakel · 2011 · Systematic Biology
34. Assessment of substitution model adequacy using frequentist and Bayesian methods
    Ripplinger, Jennifer, Sullivan, Jack · 2010 · Molecular Biology and Evolution
35. Return to Beringia: parasites reveal cryptic biogeographic history of North American pikas
    Kurt E. Galbreath, Eric P. Hoberg · 2011 · Proceedings of the Royal Society B Biological Sciences
36. Mitochondrial Gene Fragments Suggest Paraphyly of the Genus Panorpa (Mecoptera, Panorpidae)
    Bernhard Y. Misof, Dirk Erpenbeck, Klaus Peter Sauer · 2000 · Molecular Phylogenetics and Evolution
37. Comparative Phylogeography of Mesoamerican Highland Rodents: Concerted versus Independent Response to past Climatic Fluctuations
    Sullivan, Arellano, C. Paul Rogers · 2000 · The American Naturalist
38. Population genetics of the endangered South American freshwater turtle, Podocnemis unifilis, inferred from microsatellite DNA data
    Tibisay Escalona, Tag N. Engstrom, Omar Hernández, Brian C. Bock, Richard Carl Vogt, Nicole Valenzuela · 2008 · Conservation Genetics
39. A Novel Use of Equilibrium Frequencies in Models of Sequence Evolution
    Nick Goldman, Simon Whelan · 2002 · Molecular Biology and Evolution
40. Rapid radiation and cryptic speciation in mediterranean triplefin blennies (Pisces: Tripterygiidae) combining multiple genes
    Josep Carreras-Carbonell, Enrique Macpherson, Marta Pascual · 2005 · Molecular Phylogenetics and Evolution
41. Maximum Likelihood as an Alternative to Parsimony for Inferring Phylogeny Using Nucleotide Sequence Data
    Paul O. Lewis · 1998 · Springer eBooks
42. Phylogenetic Analyses of Parasites in the New Millennium
    David A. Morrison · 2006 · Advances in Parasitology/Advances in parasitology
43. Molecular Approaches to Identify Cryptic Species and Polymorphic Species within a Complex Community of Fig Wasps
    Jinhua Xiao, Ningxin Wang, Yanwei Li, Robert W. Murphy, Dong-Guang Wan, Li‐Ming Niu, Haoyuan Hu, Yueguan Fu, Da‐Wei Huang · 2010 · PLoS ONE
44. How many species are in the genus Batrachuperus? A phylogeographical analysis of the stream salamanders (family Hynobiidae) from southwestern China
    Jinzhong Fu, Xiaomao Zeng · 2008 · Molecular Ecology
45. Molecular Evidence of an African Phiomorpha–South American Caviomorpha Clade and Support for Hystricognathi Based on the Complete Mitochondrial Genome of the Cane Rat (Thryonomys swinderianus)
    Suzette K. Mouchaty, François M. Catzeflis, Axel Janke, Úlfur Árnason · 2001 · Molecular Phylogenetics and Evolution
46. PHYLOGENETIC POSITION OF THE FRESHWATER ANOMURAN FAMILY AEGLIDAE
    Marcos Pérez‐Losada, Megan L. Porter, Carlos G. Jara, Keith A Crandall, Georgina Bond‐Buckup · 2002 · Journal of Crustacean Biology
47. Origin of Chinese Goldfish and Sequential Loss of Genetic Diversity Accompanies New Breeds
    Shuyan Wang, Jing Luo, Robert W. Murphy, Shi‐Fang Wu, Chunling Zhu, Yun Gao, Ya‐Ping Zhang · 2013 · PLoS ONE
48. ModelOMatic: Fast and Automated Model Selection between RY, Nucleotide, Amino Acid, and Codon Substitution Models
    Simon Whelan, James E. Allen, Benjamin P. Blackburne, David Talavera · 2014 · Systematic Biology
49. Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations
    David Alejandro Duchêne, Sebastián Duchêne, Edward Charles Holmes, Simon Y. W. Ho · 2015 · Molecular Biology and Evolution
50. Mitochondrial DNA sequence analysis of the spectacled salamander, Salamandrina terdigitata (Urodela: Salamandridae), supports the existence of two distinct species
    Marco Mattoccia, Antonio Romano, Valerio Sbordoni · 2005 · Zootaxa
51. Site-Specific Amino Acid Replacement Matrices from Structurally Constrained Protein Evolution Simulations
    Marı́a Silvina Fornasari, Gustavo D. Parisi, Julián Echave · 2002 · Molecular Biology and Evolution
52. Can Weighting Improve Bushy Trees? Models of Cytochrome b Evolution and the Molecular Systematics of Pipits and Wagtails (Aves: Motacillidae)
    Gary Voelker, Scott V. Edwards · 1998 · Systematic Biology
53. Support for a Monophyletic Lemuriformes: Overcoming Incongruence Between Data Partitions
    Kathrin F. Stanger‐Hall, Cliff Cunningham · 1998 · Molecular Biology and Evolution
54. Phylogenomic analyses recover a clade of large-bodied decapodiform cephalopods
    Frank E. Anderson, Annie R. Lindgren · 2020 · Molecular Phylogenetics and Evolution
55. Myodocopa (Crustacea: Ostracoda) as models for evolutionary studies of light and vision: multiple origins of bioluminescence and extreme sexual dimorphism
    Todd H. Oakley · 2005 · Hydrobiologia
56. A Genetic Assessment of the Recovery Units for the Mojave Population of the Desert Tortoise, Gopherus agassizii
    Robert W. Murphy, Kristin H. Berry, Taylor Edwards, Ann M. McLuckie · 2007 · Chelonian Conservation and Biology
57. Phylogenetics, zoogeography, and the role of dispersal and vicariance in the evolution of the Rana catesbeiana (Anura: Ranidae) species group
    James D. Austin, Stephen C. Lougheed, Paul E. Moler, Peter T. Boag · 2003 · Biological Journal of the Linnean Society
58. Identifying the Best Approximating Model in Bayesian Phylogenetics: Bayes Factors, Cross-Validation or wAIC?
    Nicolas Lartillot · 2023 · Systematic Biology
59. Phylogenetic reconstruction of carnivore social organizations
    Fredrik Dalerum · 2007 · Journal of Zoology
60. Basal relationships in the Drosophila melanogaster species group
    Artyom Kopp · 2006 · Molecular Phylogenetics and Evolution
61. Phylogeny of the Dragonfly and Damselfly Order Odonata as Inferred by Mitochondrial 12S Ribosomal RNA Sequences
    Corrie Saux, Chris M. Simon, Greg S. Spicer · 2003 · Annals of the Entomological Society of America
62. Integrative taxonomy of Lepidolejeunea (Jungermanniopsida: Porellales): Ocelli allow the recognition of two neglected species
    Jochen Heinrichs, Kathrin Feldberg, Julia Bechteler, Armin Scheben, Aleksandra Czumaj, Tamás Pócs, Harald Schneider, Alfons Schäfer‐Verwimp · 2015 · Taxon
63. Major Lineages of the Genus Lilium (Liliaceae) Based on nrDNA ITS Sequences, with Special Emphasis on the Korean Species
    Chang Shook Lee, Seung‐Chul Kim, Sung Hee Yeau, Nam Sook Lee · 2011 · Journal of Plant Biology
64. Estimating selection pressures on alignments of coding sequences
    Sergei L. Kosakovsky Pond, Art F. Y. Poon, Simon D. W. Frost · 2009 · Cambridge University Press eBooks
65. Variation in the Pattern of Nucleotide Substitution Across Sites
    John P. Huelsenbeck, Rasmus Nielsen · 1999 · Journal of Molecular Evolution
66. A codon-based model designed to describe lentiviral evolution
    A. K. Pedersen, Carsten Wiuf, F. Christiansen · 1998 · Molecular Biology and Evolution
67. Phylogenetic position of the Tenrecs (Mammalia: Tenrecidae) of Madagascar based on analysis of the complete mitochondrial genome sequence of Echinops telfairi
    Suzette K. Mouchaty, Anette Gullberg, Axel Janke, Úlfur Árnason · 2000 · Zoologica Scripta
68. An unexpected recent ancestor of unisexual Ambystoma
    ALEXANDER V. ROBERTSON, Cadhla Firth, John H. Niedzwiecki, Jinzhong Fu, James P. Bogart · 2006 · Molecular Ecology
69. Affinities among Anostracan (Crustacea: Branchiopoda) Families Inferred from Phylogenetic Analyses of Multiple Gene Sequences
    Elpidio A. Remigio, Paul D. N. Hebert · 2000 · Molecular Phylogenetics and Evolution
70. Using protein structural information in evolutionary inference: transmembrane proteins
    Píetro Lió, Nick Goldman · 1999 · Molecular Biology and Evolution
71. Phylogeny of the Callandrena subgenus of Andrena (Hymenoptera: Andrenidae) based on mitochondrial and nuclear DNA data: Polyphyly and convergent evolution
    Leah L. Larkin, John L. Neff, Beryl Brintnall Simpson · 2005 · Molecular Phylogenetics and Evolution
72. Maximum‐Likelihood Analysis Using TREE‐PUZZLE
    Heiko A. Schmidt, Arndt von Haeseler · 2007 · Current Protocols in Bioinformatics
73. Molecular phylogeny of songbirds (Passeriformes) inferred from mitochondrial 16S ribosomal RNA gene sequences
    Greg S. Spicer, Leslie Dunipace · 2003 · Molecular Phylogenetics and Evolution
74. An Evolutionary Model for Protein-Coding Regions with Conserved RNA Structure
    Jakob Skou Pedersen, Roald Forsberg, Irmtraud M. Meyer, Jotun Hein · 2004 · Molecular Biology and Evolution
75. Molecular Phylogeny of Conradina and Other Scrub Mints (Lamiaceae) from the Southeastern USA: Evidence for Hybridization in Pleistocene Refugia?
    Christine E. Edwards, Pamela S. Soltis, Pamela S. Soltis · 2006 · Systematic Botany
76. NONSTOCHASTIC VARIATION OF SPECIES-LEVEL DIVERSIFICATION RATES WITHIN ANGIOSPERMS
    Hallie J. Sims, Kevin McConway · 2003 · Evolution
77. New Statistical Criteria Detect Phylogenetic Bias Caused by Compositional Heterogeneity
    David Alejandro Duchêne, Sebastián Duchêne, Simon Y. W. Ho · 2017 · Molecular Biology and Evolution
78. Phylogeny of a gastropod species flock: Exploring speciation in Lake Tanganyika in a molecular framework
    Ellinor Michel · 2000 · Advances in ecological research/Advances in Ecological Research
79. Phylogenetic relationships of tachinid flies in subfamily Exoristinae (Tachinidae: Diptera) based on 28S rDNA and elongation factor‐1α
    John O. Stireman · 2002 · Systematic Entomology
80. The “Celestial Pearl danio” is a miniature Danio (s.s) (Ostariophysi: Cyprinidae): evidence from morphology and molecules
    Kevin W. Conway, Wei‐Jen Chen, Richard L. Mayden · 2008 · Zootaxa
81. Cladogenesis and Vicariance Patterns in the Toad-Headed Lizard Phrynocephalus versicolor Species Complex
    Yuezhao Wang, Jinzhong Fu · 2004 · Copeia
82. Estimation of Phylogeny and Invariant Sites under the General Markov Model of Nucleotide Sequence Evolution
    Vivek Jayaswal, John Robinson, Lars Sommer Jermiin · 2007 · Systematic Biology
83. Molecular diversity of the 5S rRNA gene and genomic relationships in the genus Avena (Poaceae: Aveneae)
    Yuanying Peng, Yuming Wei, Bernard R. Baum, Youliang Zheng · 2008 · Genome
84. PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy
    Jeremy M. Brown, Robert ElDabaje · 2008 · Bioinformatics
85. Phylogenetic analysis of the rpoB gene from the plastid-like DNA of Plasmodium falciparum
    Malcolm J. Gardner, Nick Goldman, Phil Barnett, Peter W. Moore, Kaveri Rangachari, Malcolm Strath, Andrea Whyte, Donald H. Williamson, Robert J. Wilson · 1994 · Molecular and Biochemical Parasitology
86. REANALYSIS OF THE RELATIONSHIPS AMONG THE CIRRIPEDIA AND THE ASCOTHORACIDA AND THE PHYLOGENETIC POSITION OF THE FACETOTECTA (MAXILLOPODA: THECOSTRACA) USING 18S rDNA SEQUENCES
    Marcos Pérez‐Losada, Keith A Crandall, Gregory A. Kolbasov, Jens T. Hoeg · 2002 · Journal of Crustacean Biology
87. The Effect of Branch Length Variation on the Selection of Models of Molecular Evolution
    David Posada · 2001 · Journal of Molecular Evolution
88. A molecular phylogeny of eurytomid wasps inferred from DNA sequence data of 28S, 18S, 16S, and COI genes
    Yan Chen, Hui Faye Xiao, Jinzhong Fu, Da-Wei Huang · 2003 · Molecular Phylogenetics and Evolution
89. Molecular phylogeny and biogeography of Linanthus (Polemoniaceae)
    Charles D. Bell, Robert W. Patterson · 2000 · American Journal of Botany
90. Population structure and history of a phenotypically variable teiid lizard (Ameiva chrysolaema) from Hispaniola: the influence of a geologically complex island
    Matthew E. Gifford, Robert Powell, Allan Larson, Ronald L Gutberlet · 2004 · Molecular Phylogenetics and Evolution
91. Species Relationships in Krameria (Krameriaceae) Based on ITS Sequences and Morphology: Implications for Character Utility and Biogeography
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92. Molecular evidence to reconcile taxonomic instability in mahseer species (Pisces: Cyprinidae) of India
    Praveen Khare, Vindhya Mohindra, Anindya Sundar Barman, Rajeev K. Singh, KULDEEP KUMAR LAL · 2014 · Organisms Diversity & Evolution
93. Relative Model Fit Does Not Predict Topological Accuracy in Single-Gene Protein Phylogenetics
    Stephanie J. Spielman · 2020 · Molecular Biology and Evolution
94. Molecular Systematics and Biogeography of Crawfurdia, Metagentiana and Tripterospermum (Gentianaceae) Based on Nuclear Ribosomal and Plastid DNA Sequences
    Shengyun Chen, TAO XIA, Yujin Wang, Jianquan Liu, Shilong Chen · 2005 · Annals of Botany
95. Patterns of Speciation in the Yucca Moths: Parallel Species Radiations within the Tegeticula yuccasella Species Complex
    David M. Althoff, Kari A. Segraves, Jim Leebens‐Mack, Olle Pellmyr · 2006 · Systematic Biology
96. Molecular Evolution and Phylogeny of the buzzatii Complex (Drosophila repleta Group): A Maximum-Likelihood Approach
    Francisco Rodrı́guez-Trelles, Lourdes Alarcón, Antonio Fontdevila · 2000 · Molecular Biology and Evolution
97. Substitution Model Adequacy and Assessing the Reliability of Estimates of Virus Evolutionary Rates and Time Scales
    Sebastián Duchêne, Francesca Di Giallonardo, Edward Charles Holmes · 2015 · Molecular Biology and Evolution
98. Toward Assigning Helical Regions in Alignments of Ribosomal RNA and Testing the Appropriateness of Evolutionary Models
    Michael Schöniger, Arndt von Haeseler · 1999 · Journal of Molecular Evolution
99. Phylogenetic relationships in genus Niviventer (Rodentia: Muridae) in China inferred from complete mitochondrial cytochrome b gene
    Meidong Jing, Hon‐Tsen Yu, Sheng-Hai Wu, Wen Wang, Xiaoguang Zheng · 2007 · Molecular Phylogenetics and Evolution
100. Molecular phylogeny and a chronology of diversification for “phractocephaline” catfishes (Siluriformes: Pimelodidae) based on mitochondrial DNA and nuclear recombination activating gene 2 sequences
     Michael Hardman, John G. Lundberg · 2006 · Molecular Phylogenetics and Evolution