The evolution of non-coding chloroplast DNA and its application in plant systematics

Annals of the Missouri Botanical Garden

Volumn 87, Issue 4, 2000, Pages 482-498

  Kelchner, S A ^a  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

Alignment; Intergenic spacers; Introns; Molecular evolution; Mutational biases; Mutational mechanisms; Phylogenetic analysis; Secondary structure

Indexed keywords

EID: 0034491886     PISSN: 00266493     EISSN: None     Source Type: Journal    
DOI: 10.2307/2666142     Document Type: Article

References (118)

1. The role of insertion/deletions in the evolution of the intergenic region between pbsA and trnH in the chloroplast genome
2. Chloroplast DNA characters, phylogeny, and classification of Lathyrus (Fabaceae)
3. The ITS region of nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny
4. Biogeography and floral evolution of baobabs (Adansonia, Bombacaceae) as inferred from multiple data sets
5. A phylogenetic analysis of Epilobium (Onagraceae) based on nuclear ribosomal DNA sequences
6. Tribal phylogeny of the Asteraceae based on two non-coding chloroplast sequences, the trnL intron and trnL/trnF intergenic spacer
7. Phylogeny of South African Gnaphalieae (Asteraceae) based on two non-coding chloroplast sequences
8. Variation in copy number of a 24-base pair tandem repeat in the chloroplast DNA of Oenothera hookeri strain Johansen
9. Non-coding chloroplast DNA for plant molecular systematics at the infrageneric level
10. Island colonization and evolution of the insular woody habit in Echium L. (Boraginaceae)
11. Nucleotide sequence of the split tRNA(Leu/UAA) gene from Vicia faba chloroplasts: Evidence for structural homologies of the chloroplast tRNA(Leu) intron with the intron from the autosplicable Tetrahymena ribosomal RNA precursor
12. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction
13. Branch support and tree stability
14. Bootstrap hypothesis tests for evolutionary trees and other dendrograms
15. Length heteroplasmy of sturgeon mitochondrial DNA: An illegitimate elongation model
16. Self-splicing of Group I introns
17. Chloroplast DNA and the study of plant phylogeny: Present status and future prospects
18. Processes of chloroplast DNA evolution
19. Rates and patterns of chloroplast DNA evolution
20. Phylogenetic analysis of chloroplast DNA variation in Coffea L
21. Slipped-strand mispairing in a plastid gene: rpoC2 in grasses (Poaceae)
22. Molecular evolution of chloroplast DNA sequences
23. Quantification of base substitutions in eukaryotic 5S rRNA: Selection for the maintenance of RNA secondary structure
24. Ribosomal RNA secondary structure: Compensatory mutations and implications for phylogenetic analysis
25. Phylogenetic relationships of Dipsacales based on rbcL sequences
26. Phylogenetic analysis of Apiaceae subfamily Apioideae using nucleotide sequences from the chloroplast rpoC1 intron
27. Multiple independent losses of the rpoC1 intron in angiosperm chloroplast DNA's
28. Molecular systematics of Apiaceae subfamily Apioideae: Phylogenetic analyses of nuclear ribosomal DNA internal transcribed spacer and plastid rpoC1 intron sequences
29. Group I introns as mobile genetic elements: Facts and mechanistic speculations - A review
30. Association between chloroplast and mitochondrial lineages in oaks
31. Parsimony jackknifing outperforms neighbor-joining
32. Evolutionary trees from DNA sequences: A maximum likelihood approach
33. Confidence limits on phylogenies: An approach using the bootstrap
34. Using chloroplast DNA to trace postglacial migration routes of oaks into Britain
35. The use of chloroplast DNA to resolve plant phylogenies: Non-coding versus rbcL sequences
36. Evolution of a non-coding region of the chloroplast genome
37. Molecular evolution of non-coding regions of the chloroplast genome in the Crassulaceae and related species
38. The contribution of slippage-like processes to genome evolution
39. Phylogenetic evidence for horizontal transmission of Group I introns in the nuclear ribosomal DNA of mushroom-forming fungi
40. CLUSTAL V: Improved software for multiple sequence alignment
41. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis
42. Columbines: A geographically widespread species flock
43. Phylogeny of the Proteaceae based on atpB and atpB-rbcL intergenic spacer region sequences
44. Structural rearrangements, including parallel inversions, within the chloroplast genome of Anemone and related genera
45. The endpoints of an inversion in wheat chloroplast DNA are associated with short repeated sequences containing homology to att-lambda
46. The performance of phylogenetic methods in simulation
47. Improved predictions of secondary structures for RNA
48. matK DNA sequences and phylogenetic reconstruction in Saxifragaceae s. str.
49. Low levels of intraspecific genetic variation at a rapidly evolving chloroplast DNA locus in North American duckweeds (Lemnaceae)
50. Evolution of protein molecules
51. Molecular phylogeny of Dipterocarpaceae in Southeast Asia based on nucleotide sequences of matK, trnL intron, and trnL-trnF intergenic spacer region in chloroplast DNA
52. Comparative studies of the structure of chloroplast DNA from four species of Oryza: Cloning and physical maps
53. Variations in chloroplast DNA from rice (Oryza sativa): Differences between deletions mediated by short direct-repeat sequences within a single species
54. Molecular evolution and phylogenetic utility of the chloroplast rpl16 intron in Chusquea and the Bambusoideae (Poaceae)
55. Hairpins create minute inversions in non-coding regions of chloroplast DNA
56. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
57. Ordered processing and splicing in a polycistronic transcript in liverwort chloroplasts
58. A simulation of phylogeny algorithms under equal and unequal evolutionary rates
59. Constraints on the evolution of plastid introns: The group II intron in the gene encoding tRNA-Val(UAC)
60. Slipped-strand mispairing: A major mechanism for DNA sequence evolution
61. Phylogeny and classification of Fumariaceae, with emphasis on Dicentra s.l., based on the plastid gene rps16 intron
62. Sedum surculosum and S. jaccardianum (Crassulaceae) share a unique 70bp deletion in the chloroplast DNA trnL(UAA)-trnF(GAA) intergenic spacer
63. Conservation of RNA secondary structures in two intron families including mitochondrial-, chloroplast-, and nuclear-encoded members
64. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis
65. Comparative and functional anatomy of group II catalytic introns - A review
66. Dispersed repeats and structural reorganization in subclover chloroplast DNA
67. Cladistic analysis of molecular and morphological data
68. Decay analysis of large sets of phylogenetic data
69. Neighboring base composition and transversion/transition bias in a comparison of rice and maize chloroplast non-coding regions
70. Neighboring base composition is strongly correlated with base substitution bias in a region of the chloroplast genome
71. A chloroplast DNA mutational hotspot and gene conversion in a non-coding region near rbcL in the grass family (Poaceae)
72. The influence of specific neighboring bases on substitution bias in noncoding regions of the plant chloroplast genome
73. Phylogeny of the Rubiaceae-Rubioideae, in particular the tribe Rubieae: Evidence from a non-coding chloroplast DNA sequence
74. Intramolecular recombination of chloroplast genome mediated by short direct-repeat sequences in wheat species
75. Chloroplast DNA systematics: A review of methods and data analysis
76. Patterns of sequence evolution and implications for parsimony analysis of chloroplast DNA
77. Relationships of the Buddlejaceae s.l. investigated using parsimony jackknife and branch support analysis of chloroplast ndhF and rbcL sequence data
78. Chloroplast rps16 intron phylogeny of the tribe Sileneae (Caryophyllaceae)
79. Comparative organization of chloroplast genomes
80. Chloroplast DNA evolution and biosystematic uses of chloroplast DNA variation
81. Plastid chromosomes: Structure and evolution
82. Chloroplast DNA variation and evolution in Pisum: Patterns of change and phylogenetic analysis
83. Unusual structure of geranium chloroplast DNA: A triple-sized inverted repeat, extensive gene duplications, multiple inversions, and two repeat families
84. Phylogenetic analysis of the Triticeae (Poaceae) based on rpoA sequence data
85. Molecular cloning and complete nucleotide sequence of the repeated unit and flanking gene of the scallop Pecten maximus mitochondrial DNA: Putative replication origin features
86. Polymorphism, hybridization, and variable evolutionary rate in molecular phylogenies
87. A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA
88. The neighbor-joining method: A new method for reconstructing phylogenetic trees
89. Phylogeny of some species of Cyrtandra (Gesneriaceae) inferred from the atpB/rbcL cpDNA intergene region
90. Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae)
91. Polyphyletism of Celastrales deduced from a chloroplast noncoding DNA region
92. Cladistic biogeography of Gleditsia (Leguminosae) based on ndhF and rpl16 chloroplast gene sequences
93. Molecular phylogeny of Nothofagus (Nothofagaceae) based on the atpB-rbcL intergenic spacer of the chloroplast DNA
94. Fine structural features of the chloroplast genome: Comparison of the sequenced chloroplast genomes
95. The tortoise and the hare: Choosing between noncoding plastome and nuclear ADH sequences for phylogeny reconstruction in a recently diverged plant group
96. Molecular evolution of 18S rDNA in angiosperms: Implications for character weighting in phylogenetic analysis
97. Discordance between ITS and chloroplast topologies in the Boykinia group (Saxifragaceae)
98. Angiosperm phylogeny inferred from 18S ribosomal DNA sequences
99. Deletions/insertions, short inverted repeats, sequences resembling att-lambda, and frame-shifted-mutated open reading frames are involved in chloroplast DNA differences in the genus Oenothera subsection Munzia
100. Mechanisms of spontaneous and induced frameshift mutation in bacteriophage T4
101. Among-site rate variation and phylogenetic analysis of 12S rRNA in Sigmodontine rodents
102. The effect of topology on estimates of among-site rate variation
103. Estimation of evolutionary distance between nucleotide sequences
104. Relative efficiencies of the maximum likelihood, neighbor joining, and maximum parsimony methods when substitution rate varies with site
105. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
106. Randomization confounded: A response to Carpenter
107. Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA
108. Paired sequence difference in ribosomal RNAs: Evolutionary and phylogenetic implications
109. Elision: A method for accommodating multiple molecular sequence alignments with alignment-ambiguous sites
110. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs
111. Evidence for replication slippage in the evolution of Oenothera chloroplast DNA
112. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
113. Among-site rate variation and its impact on phylogenetic analyses
114. Estimation of the transition/transversion rate bias and species sampling
115. Maximum likelihood trees from DNA sequences: A peculiar statistical estimation problem
116. On finding all suboptimal foldings of an RNA molecule
117. Evolution of higher-plant chloroplast DNA-encoded genes: Implications for structure-function and phylogenetic studies