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Microstructural Changes in Noncoding Chloroplast DNA: Interpretation, Evolution, and Utility of Indels and Inversions in Basal Angiosperm Phylogenetic Inference
43/43 checkable references clean · checked 2026-10-16
Every reference with a DOI or an arXiv id in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.
11 with no DOI or arXiv id: not checked. A reference deposited without a DOI is checked only when it names an arXiv id, under that id’s DataCite DOI. The rest are never matched by title or guessed at; they stay outside the checked set, and this line says so.
The 43 checked references that resolve
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Data Decisiveness, Data Quality, and Incongruence in Phylogenetic Analysis: An Example From the Monocotyledons Using Mitochondrial atp A Sequences
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Phylogenetic Analysis of Apiaceae Subfamily Apioideae Using Nucleotide Sequences from the ChloroplastrpoC1 Intron
resolves10.2307/2446441
Molecular systematics of Apiaceae subfamily Apioideae: phylogenetic analyses of nuclear ribosomal DNA internal transcribed spacer and Plastid <i>rpoC1</i> intron sequences
resolves10.1006/mpev.1993.1015
Alignment-Ambiguous Nucleotide Sites and the Exclusion of Systematic Data
resolves10.1007/s002940050517
Evolutionary significance of an unusual chloroplast DNA inversion found in two basal angiosperm lineages
resolves10.1007/BF00164032
The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment
resolves10.1006/mpev.1999.0709
How Slippage-Derived Sequences Are Incorporated into rRNA Variable-Region Secondary Structure: Implications for Phylogeny Reconstruction
resolves10.1093/oxfordjournals.molbev.a025552
Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA
resolves10.1071/SB98027
Phylogeny of the Proteaceae based on
<i>atpB</i>
and
<i>atpB</i>
-
<i>rbcL</i>
intergenic spacer region sequences
resolves10.1073/pnas.84.16.5818
A chloroplast DNA inversion marks an ancient evolutionary split in the sunflower family (Asteraceae)
resolves10.2307/2399875
Phylogenetic Inference in Saxifragaceae Sensu Stricto and Gilia (Polemoniaceae) Using matK Sequences
resolves10.1006/mpev.1997.0432
Molecular Evolution and Phylogenetic Utility of the Chloroplastrpl16Intron inChusqueaand the Bambusoideae (Poaceae)
resolves10.1007/s002940050130
Hairpins create minute inversions in non-coding regions of chloroplast DNA
resolves10.1006/mpev.1995.1028
Use of rRNA Secondary Structure in Phylogenetic Studies to Identify Homologous Positions: An Example of Alignment and Data Presentation from the Frogs
resolves10.1126/science.286.5441.947
The Root of Angiosperm Phylogeny Inferred from Duplicate Phytochrome Genes
resolves10.1016/0378-1119(89)90026-7
Comparative and functional anatomy of group II catalytic introns — a review
resolves10.1007/BF00336789
A chloroplast DNA mutational hotspot and gene conversion in a noncoding region near rbcL in the grass family (Poaceae)
resolves10.2307/2656601
Intra‐ and interspecific phylogeny of wild <i>Fagopyrum</i> (Polygonaceae) species based on nucleotide sequences of noncoding regions in chloroplast DNA
resolves10.1006/mpev.1999.0769
The Phylogeny of the Asteridae sensu lato Based on Chloroplast ndhF Gene Sequences
resolves10.2307/2399876
Evidence for the Polyphyly of the Scrophulariaceae Based on Chloroplast rbcL and ndhF Sequences
resolves10.1016/S0960-9822(00)80119-0
Multigene analyses identify the three earliest lineages of extant flowering plants
resolves10.1038/46536
The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes
resolves10.1126/science.255.5052.1697
Chloroplast DNA Evidence on the Ancient Evolutionary Split in Vascular Land Plants
resolves10.2307/2446155
Chloroplast DNA phylogeny, reticulate evolution, and biogeography of
<i>Paeonia</i>
(Paeoniaceae)
resolves10.2307/2446640
The tortoise and the hare: choosing between noncoding plastome and nuclear <i>Adh</i> sequences for phylogeny reconstruction in a recently diverged plant group
resolves10.1038/46528
Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology
resolves10.1016/0092-8674(87)90600-3
Control of plastid gene expression: 3′ inverted repeats act as mRNA processing and stabilizing elements, but do not terminate transcription
resolves10.1093/nar/22.22.4673
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
resolves10.1007/BF00163848
Inching toward reality: An improved likelihood model of sequence evolution
resolves10.1007/BF00351678
Molecular evolution of noncoding regions of the chloroplast genome in the Crassulaceae and related species
resolves10.1007/BF00339624
Deletions/insertions, short inverted repeats, sequences resembling att-lambda, and frame shift mutated open reading frames are involved in chloroplast DNA differences in the genus Oenothera subsection Munzia
resolves10.1073/pnas.84.24.9054
Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs.
resolves10.1006/mpev.1999.0729
Phylogeny of the Grass Family (Poaceae) from rpl16 Intron Sequence Data
resolves10.1007/s002399910036
A Phylogenetic Perspective on Sequence Evolution in Microsatellite Loci
The 11 references with no DOI or arXiv id, listed, not checked
no DOI — not checkedPhD diss
no DOI — not checkedR Schneider, P Bork, D Brutlag, J Glasgow, H‐W Mewes, R Zimmer, eds. Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
no DOI — not checkedPhD diss
no DOI — not checkedMolecular systematics of plants
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no DOI — not checkedrf31
no DOI — not checkedanalysis of phylogeny and character evolution
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