The cytochrome b gene as a phylogenetic marker: The limits of resolution for analyzing relationships among cichlid fishes

Journal of Molecular Evolution

Volumn 53, Issue 2, 2001, Pages 89-103

  Farias, Izeni P ^a,d   Ortí, Guillermo ^b   Sampaio, Iracilda ^c   Schneider, Horacio ^c   Meyer, Axel ^d  

^a FEDERAL UNIVERSITY OF AMAZONAS   (Brazil)

^b UNIVERSITY OF NEBRASKA   (United States)

^c FEDERAL UNIVERSITY OF PARÁ   (Brazil)

^d UNIVERSITY OF KONSTANZ   (Germany)

Author keywords

Cichlid fishes; Cytochrome b; DNA substitution rate; Long branches; Phylogeny; Systematics

Indexed keywords

CYTOCHROME B;

ARTICLE; CODON; FISH; GENE MAPPING; NONHUMAN; PHYLOGENY; SEQUENCE ANALYSIS; TAXONOMY;

EID: 0034943229     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002390010197     Document Type: Article

References (92)

1. Limitations of metazoan 18S rRNA sequence data: Implications for reconstructing a phylogeny of the animal kingdom and inferring the reality of the cambrian explosion
2. Are third position really that bad? A test using vertebrate cytochrome b
3. Quantification of homoplasy for nucleotide transitions and transversions and a reexamination of assumptions in weighted parsimony analysis
4. Mitochondrial of DNA sequences of primates: Tempo and mode of evolution
5. Evolutionary analysis of cytochrome b sequences in some Perciformes: Evidence for a slower rate of evolution than in mammals
6. Patterns of evolutionary divergence in arboreal Amazonian echimyid rodents: The perspective of mtDNA sequence variation
7. Mitochondrial resolution of a deep branch in the genealogical tree for perching birds
8. Mitochondrial cytochrome b: Evolution and structure of the protein
9. Molecular phylogeny of neotropical cichlids: The relationships of cichlasomines and heroines
10. Mitochondrial DNA phylogeny of the family Cichlidae: Monophyly and fast molecular evolution of the neotropical assemblage
11. Total evidence: Molecules, morphology, and the phylogenetics of cichlids fishes
12. Testing significance of incongruence
13. Constructing a significance test for incongruence
14. The retention index and rescaled consistency index
15. Phylogenies and the comparative method
16. The phylogenetic utility of cytochrome b: Lessons from bufonid frogs
17. Correlation of functional domains and rates of nucleotide substitution in cytochrome b
18. Molecular phylogenetics of finches and sparrows: Consequences of character state removal in cytochrome b sequences
19. Nucleotide substitution models and estimation of phylogeny
20. Signal, noise, and reliability in molecular evolutionary analyses
21. Mammalian mitochondrial DNA evolution: A comparison of the cytochrome b and cytochrome c oxidase II genes
22. Evolution of cytochrome b gene in mammals
23. A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene
24. Phylogenetic analysis: Concepts and methods
25. Relationships among cave swallow populations (Petrochelidon fulva) determined by comparisons of microsatellite and cytochrome b data
26. Quantitative phyletics and the evolution of anurans
27. Total evidence or taxonomic congruence: Cladistics or consensus classification
28. Dynamics of mtDNA evolution in animals: Amplification and sequencing with conserved primers
29. Evolution of higher-organism DNA
30. Pathways of lysozyme evolution inferred from the sequences of cytochrome b in birds
31. A phylogeny and classification of the South American Cichlidae (Teleoster: Perciformes)
32. Molecular phylogeny of osteoglossoids: A new model for Gondwanian origin and plate tectonic transportation of the Asian arowana
33. A molecular phylogeny of the gopher tortoises, with comments on familial relationships within the Testudinoidea
34. Molecular systematics, biogeography, and population structure of neotropical freshwater needle-fishes of the genus Potamorrhaphis
35. The phylogenetic utility of the mitochondrial cytochrome b gene for inferring relationships among actinopterygian fishes
36. Branch length heterogeneity leads to nonindependent branch length estimates and can decrease the efficiency of methods of phylogenetic inference
37. Body size, metabolic rate, generation time, and the molecular clock
38. Systematics and evolution of lower Central American cichlids inferred from analysis of cytochrome b gene sequence
39. Evolution of mitochondrial DNA in fishes
40. Shortcomings of the cytochrome b gene as a molecular marker
41. Origin of tetrapods inferred from their mitochondrial DNA affiliation to lungfish
42. Monophyletic origin of Lake Victoria cichlid fishes suggested by mitochondrial DNA sequences
43. African fishes - A replay
44. Ribosomal RNA in vertebrates: Evolution and phylogenetic applications
45. Testing species phylogenies and phylogenetic methods with congruence
46. The window of taxonomic resolution for phylogenies based on mitochondrial cytochrome b
47. Nuclear gene introns versus mitochondrial genes as molecular clocks
48. Evolutionary relationships within the Ensatina eschscholtzii complex confirm the ring species interpretation
49. Hydrophobicity and phylogeny
50. Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences
51. Phylogenetic relationships of neopterygian fishes, inferred from mitochondrial DNA sequences
52. Body size effects and rates of cytochrome b evolution in tube-nosed seabirds
53. Population size and rate of evolution
54. The nearly neutral theory of molecular evolution
55. Global survey of mitochondrial DNA sequences in the threespine stickleback: Evidence for recent migration
56. Molecular evolution of ependymin and the phylogenetic resolution of early divergences among teleost fishes
57. The radiation of characiform fishes and the limits of resolution of mitochondrial ribosomal DNA sequences
58. Amplifying ancient DNA
59. Model Test: Testing the model of DNA substitution
60. Comparative evolution of the mitochondrial cytochrome b gene and nuclear β-fibrinogen intron 7 in woodpeckers
61. Thermal habit, metabolic rate, and evolution of mitochondrial DNA
62. Molecular systematic of Middle American cichlid fishes and evolution of trophic-types in 'Cichlasoma (Amphilophus)' and C. (Thorichthys)
63. Molecular evolution, systematics, and zoogeography of the rockfish subgenus Sebastomus (Sebastes, Scorpaenidae) based on mitochondrial cytochrome b and control region sequences
64. A simple method for estimating and testing minimum-evolution trees
65. Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants
66. Phylogenetic intrarelationships of the family Cichlidae: An overview
67. Reconstructing labroid evolution with single-copy nuclear DNA
68. Quartet puzziling: A quartet maximum likelihood method for reconstructing tree topologies
69. Genetic divergence, speciation, and morphological stasis in a lineage of African cichlid fishes
70. Mitochondrial phylogeny of the endemic mouthbrooding lineages of cichlid fishes of Lake Tanganyika. East Africa
71. Mitochondrial phylogeny of the Lamprologini, the major substrate spawning lineage of cichlid fishes from Lake Tanganyika in Eastern Africa
72. Among-site rate variation and phylogenetic analysis of 12S rRNA in sigmodontine rodents
73. Unusual mitochondrial DNA polymorphism in two local populations of blue tit (Parus caerulens)
74. Phylogenetic test of the molecular clock and linearized trees
75. Molecular phylogeny of North Mediterranean freshwater barbs (genus Barbus: Cyprinidae) inferred from cytochrome b sequences: Biogeographic and systematic implications
76. Evolutionary relationships among the eukaryotic crown taxa taking into account site-to-site rate variation in 18S rRNA
77. Can weighting improve bushy trees? Models of cytochrome b evolution and the molecular systematics of pipits and wagtails (Aves: Motacillidae)
78. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
79. Among-site rate variation and its impact on phylogenetic analyses
80. Molecular evolutionary dynamics of cytochrome b in Strepsirrhine primates: The phylogenetic significance of third-position transversions
81. The largemouth bass cytochrome b gene
82. War of the iguanas: Conflicting molecular and morphological phylogenies and long-branch attractions in Iguanid lizards
83. Ecomorphological diversification and convergence in fluvial cichlid fishes
84. Evolutionary conservation of microsatellite flanking regions and their use in resolving the phylogeny of cichlid fishes (Pisces: Perciformes)
85. Searching for the closest living relative(s) of tetrapods through evolutionary analyses of mitochondrial and nuclear data
86. Evolutionary relationships of the coelacanth, lungfishes, and tetrapods based on the 28S ribosomal RNA gene
87. Molecular evidence on the evolutionary and biogeographical patterns of European cyprinids