Microstructural Changes in Noncoding Chloroplast DNA: Interpretation, Evolution, and Utility of Indels and Inversions in Basal Angiosperm Phylogenetic Inference

By S. Graham, P. Reeves, Analiese C. E. Burns, Richard E. Olmstead. INTERNATIONAL JOURNAL PLANT SCIENCES, 2000

267 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e1f511effa136887cb5c4ab62fa6df8c9eecbf29

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Citations in the corpus

Diversity and origin of cultivated and citron type watermelon (Citrullus lanatus) (2007, background): “Insertion/deletion events (indels) that were potentially parsimonious were scored and added to the end of the data sets as single binary (0 vs. 1) characters (Graham et al. 2000).”
Multiple Multilocus DNA Barcodes from the Plastid Genome Discriminate Plant Species Equally Well (2008, background): “, [31]), potentially yielding polymorphisms within one or more species.”
Choosing and Using a Plant DNA Barcode (2011, background): “Microinversions are not uncommon [31], and these may need accounting for (detection/reorientation/removal) in data analyses as homoplastic microinversions can lead to over-estimates of genetic differences between samples and thus to erroneous groupings of unrelated sequences [31,32], although in som”
Phylogeny of Nymphaea (Nymphaeaceae): Evidence from Substitutions and Microstructural Changes in the Chloroplast trnT‐trnF Region (2007, background): “Compared with larger data sets of noncoding sequences analyzed so far, similar observations were made by Graham et al. (2000) for the slowly evolving chloroplast (cp) inverted repeat (IR) and by Löhne and Borsch (2005) for the rapidly evolving group II intron in chloroplast petD.”
Evolution of Endosperm Developmental Patterns among Basal Flowering Plants (2000, background): “…Nixon et al. 1994; Nandi et al. 1998; Soltis et al. 1998, 1999, 2000; Hoot et al. 1999; Mathews and Donoghue 1999; Parkinson et al. 1999; Doyle and Endress 2000; Graham et al. 2000), and this has resulted in tremendous improvement in our understanding of the relationships of basal angiosperms.”
Phylogenetic analysis of morphology in Prunus reveals extensive homoplasy (2006, background): “Using indels in phylogenetic analyses can be beneficial because they tend to be less homoplastic than sequence data and increase resolution of consensus trees ( Graham et al. 2000, Simmons et al. 2001).”
Geographic structure, genetic diversity and source tracking of Spartina alterniflora (2007, background): “While this approach does not present all potential pathways among haplotypes, and contrasts slightly with other approaches of differentiating haplotypes based solely on the presence and absence of indels (Graham et al., 2000), it effectively portrays levels of diversity within haplotype groups delin”
Phylogenetic relationships in subtribe Poinae (Poaceae, Poeae) based on nuclear ITS and plastid trnT-trnL-trnF sequences (2008, methodology): “Unambiguous parsimony informative insertions and deletions (indels) were coded as separate presence/absence characters using the simple indel coding method of Simmons and Ochoterena (2000), with overlapping indels coded as in Graham et al. (2000) .”
The Flowers in Extant Basal Angiosperms and Inferences on Ancestral Flowers (2001, background): “…extant angiosperms, followed by Nymphaeales and a clade comprising Austrobaileyacae, Trimeniaceae, and Illiciales; this basal grade was termed the ANITA grade (Mathews and Donoghue 1999, 2000; Qiu et al. 1999, 2000, 2001; Soltis et al. 1999, 2000a; Graham and Olmstead 2000; Graham et al. 2000).”
Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA (2009, background): “Alignment rules have been proposed by Graham et al. (2000), Kelchner (2000), Borsch et al. (2003), and Löhne and Borsch (2005), largely based on inferred types of microstructural mutations.”
A 567‐Taxon Data Set for Angiosperms: The Challenges Posed by Bayesian Analyses of Large Data Sets (2007, background): “…as sister to all other angiosperms (e.g., Mathews and Donoghue 1999; 152 INTERNATIONAL JOURNAL OF PLANT SCIENCES Parkinson et al. 1999; Qiu et al. 1999, 2000, 2005; Soltis et al. 1999, 2000a; Graham et al. 2000; Zanis et al. 2002, 2003; Borsch et al. 2003; Hilu et al. 2003; Kim et al. 2004).”
Phylogeny of Aristolochiaceae based on parsimony, likelihood, and Bayesian analyses of trnL-trnF sequences (2004, methodology): “The coding strategy for indels followed ideas expressed by Graham et al. (2000) , Kelchner (2000), and Simmons and Ochoterena (2000).”
Inference of higher-order conifer relationships from a multi-locus plastid data set (2008, methodology): “…basecalling using Sequencher 4.1 (Gene Codes Corporation; Ann Arbor, Mich.), and added new sequences to an alignment (Graham et al. 2006) that includes sequences generated for previous studies of seed-plant phylogeny (Graham and Olmstead, 2000a, 2000b; Graham et al. 2000; Rai et al. 2003).”
Phylogenetic Analysis of the Plastid Inverted Repeat for 244 Species: Insights into Deeper-Level Angiosperm Relationships from a Long, Slowly Evolving Sequence Region (2011, background): “Cai Z, M Guisinger, HG Kim, E Ruck, JC Blazier, V McMurtry, JV Kuehl, J Boore, RK Jansen 2008 Extensive reorganization of the plastid genome of Trifolium subterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions.”