The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support

Molecular Biology and Evolution

Volumn 19, Issue 4, 2002, Pages 394-405

  Buckley, Thomas R ^a,b   Cunningham, Clifford W ^a  

^a DUKE UNIVERSITY   (United States)

^b LANDCARE RESEARCH   (New Zealand)

Author keywords

AIC; Maximum likelihood; Model selection; Nonparametric bootstrapping; Nucleotide substitution models; Phylogenetics

Indexed keywords

NUCLEOTIDE;

ACCURACY; ARTICLE; GENOME; HYPOTHESIS; INTERMETHOD COMPARISON; MAXIMUM LIKELIHOOD METHOD; MOLECULAR MODEL; MOLECULAR PHYLOGENY; NONHUMAN; NONPARAMETRIC TEST; NUCLEIC ACID BASE SUBSTITUTION; PARSIMONY ANALYSIS; PHYLOGENY;

EID: 0036213207     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a004094     Document Type: Article

References (93)

1. Information theory as an extension of the maximum likelihood principle
2. Testing phylogenetic approaches with empirical data, as illustrated with the parsimony method
3. Confidence intervals of evolutionary distances between sequences and comparison with usual approaches including the bootstrap method
4. Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (Family Leviviridae)
5. Gene translocation links insects and crustaceans
6. Topological bias and inconsistency of maximum likelihood using wrong models
7. 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
8. Model uncertainty, data mining and statistical inference
9. Avian evolution, Gondwana biogeography and the cretaceous-tertiary mass extinction event
10. Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods
11. Best-fit maximum likelihood models for phylogenetic inference: Empirical tests with known phylogenies
12. Bootstrap methods: Another look at the jack-knife
13. Bootstrap confidence levels for phylogenetic trees
14. Cases in which parsimony or compatibility methods will be positively misleading
15. Evolutionary trees from DNA sequences: A maximum likelihood approach
16. Confidence limits on phylogenies: An approach using the bootstrap
17. Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull
18. Toward defining the course of evolution: Minimum change for a specific tree topology
19. Key concepts in model selection: Performance and generalizability
20. Evolution of the mitochondrial cytochrome oxidase II gene in collembola
21. Ribosomal DNA phylogeny of the major extant arthropod classes and the evolution of myriapods
22. Arthropod rDNA phylogeny revisited: A consistency analysis using Monte Carlo simulation
23. Mitochondrial genes collectively suggest the paraphyly of crustaceans with respect to Insecta
24. Rooting a phylogeny with homologous genes on opposite sex chromosomes (gametologs): A case study using avian CHD
25. Arthropod phylogeny based on eight molecular loci and morphology
26. Statistical tests of models of DNA substitution
27. Toward a phylogenetic classification of primates based on DNA evidence complemented by fossil evidence
28. Basal divergences in birds and the phylogenetic utility of the nuclear RAG-1 gene
29. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites
30. Dating of the human-ape split by a molecular clock by mitochondrial DNA
31. Molecular phylogeny and evolution of primate mitochondrial DNA
32. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis
33. Systematic bias in phylogenetic analysis: Is the Strepsiptera problem solved?
34. Success of phy logenetic methods in the four-taxon case
35. Mitochondrial protein phylogeny joins myriapods with chelicerates
36. Evolutionary relationships between dinoflagellates bearing obligate diatom endosymbionts: Insight into tertiary endosymbiosis
37. Evolution of protein molecules
38. Dynamically heterogenous partitions and phylogenetic inference: An evaluation of analytical strategies with cytochrome b and ND6 gene sequences in cranes
39. Forty years insect phylogenetic systematics. Hennigs Kritische Bemerkungen, and subsequent development
40. Tree robustness and clade significance
41. Evolution of chlorophyll and bacteriochlorophyll: The problem of invariant sites in sequence evolution
42. C-mos variation in songbirds: Molecular evolution, phylogenetic implications, and comparisons with mitochondrial differentiation
43. Model selection and accounting for model uncertainty in graphical models using Occam's window
44. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes
45. Molecular phylogenetics and the origins of placental mammals
46. Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences
47. Catarrhine phylogeny: Noncoding DNA evidence for a diphyletic origin of the mangabeys and for a human-chimpanzee clade
48. Modeltest: Testing the model of DNA substitution
49. Phylogenetic relationships and rates of evolution in birds
50. Molecular phylogeny of the major arthropod groups indicates polyphyly of crustaceans and a new hypothesis for the origin of hexapods
51. Elongation factor-2: A useful gene for arthropod phylogenetics
52. Complete mitochondrial DNA sequence of the fat doormouse Glis glis: Further evidence for rodent paraphyly
53. Long-branch attraction phenomenon and the impact of among-site rate variation on rodent phylogeny
54. Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny
55. The neighbor-joining method: A new method for reconstructing phylogenetic trees
56. Confidence limits on phylogenies: The bootstrap revisited
57. Objections to bootstrapping phylogenies: A critique
58. Parametric phylogenetics?
59. DNA archives and our nearest relative: The trichotomy problem revisited
60. Phylogenetic analysis of arthropods using two nuclear protein-encoding genes supports a crustacean+hexapod clade
61. Statistical aspects of model selection
62. Primate phylogeny: Morphological vs molecular results
63. Success of parsimony in the four-taxon case: Long-branch repulsion by likelihood in the Farris zone
64. Long-branch abstractions
65. Support for a monophyletic Lemuriformes: Overcoming incongruence between data partitions
66. Ratites as oldest offshoot of avian stem - Evidence from α-crystallin A sequences
67. Parsimony, likelihood, and the role of models in molecular phylogenetics
68. Among-site rate variation and phylogenetic analysis of 12S rRNA in sigmodontine rodents
69. Phylogeography and molecular systematics of the Peromyscus aztecus species group (Rodentia: Muridae) inferred using parsimony and likelihood
70. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics
71. Phylogenetic inference
72. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood
73. Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used
74. Accounting for evolutionary rate variation among sequence sites consistently changes universal phylogenies deduced from rRNA and protein-coding genes
75. The early history of modern birds inferred from DNA sequences of nuclear and ribosomal genes
76. Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid-invariant sites-logDet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo, and elephant
77. General time-reversible distances with unequal rates across sites: Mixing Γ and inverse Gaussian distributions with invariant sites
78. Bayesian model selection and model averaging
79. The Strepsiptera problem: Phylogeny of the holometabolous insect orders inferred from 18S and 28S ribosomal sequences and morphology
80. The complete sequence of the mitochondrial genome of the crustacean Penaeus monodon: Are Malacostracan crustaceans more closely related to insects than to branchiopods?
81. Phylogenetic relationships among horseshoe crabs species: Effect of substitution models on phylogenetic analyses
82. Estimating the pattern of nucleotide substitution
83. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
84. Phylogenetic analysis using parsimony and likelihood methods
85. PAML: A program for phylogenetic analysis by maximum likelihood
86. How often do wrong evolutionary models produce better phylogenies
87. Maximum likelihood trees from DNA sequences: A peculiar statistical estimation problem
88. Phylogenetic affinities of tarsier in the context of primate Alu repeats