The Evolution of Non-Coding Chloroplast DNA and Its Application in Plant Systematics

By S. Kelchner. 2000

695 citations recorded by the source corpus.

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

View Paper: https://www.semanticscholar.org/paper/05ca2b1807e26a223ba349448a58db739f5fdd74

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology, Evolution, Behavior and Systematics

1. Thomas Borsch
2. J. Doyle
3. Pamela S. Soltis
4. D. Soltis
5. Mark W. Chase
6. D. Quandt
7. B. Guzmán
8. P. Vargas

In Molecular Biology

1. Thomas Borsch
2. J. Doyle
3. Pamela S. Soltis
4. D. Soltis
5. Mark W. Chase
6. D. Quandt
7. P. Vargas
8. Cornelia Löhne

Citations in the corpus

• Phylogenetic patterns in the fleshy-fruited Myrtaceae – preliminary molecular evidence (2005, methodology): “Sequences were aligned by eye following the guidelines of Kelchner (2000).”
• Long‐distance colonization of the Western Mediterranean by Cistus ladanifer (Cistaceae) despite the absence of special dispersal mechanisms (2009, background): “Simmons & Ochoterena’s (2000) ‘simple indel coding’ approach was followed to remove mononucleotide repeat stretches (poly-T and poly-A) because homology is highly uncertain for this type of polymorphism (Kelchner, 2000).”
• Phylogenetic relationships and taxonomy of subfamily Zygophylloideae (Zygophyllaceae) based on molecular and morphological data (2003, methodology): “Alignment of the data set was done manually following the guidelines of Kelcher (2000).”
• Paraphyly of Tarasa (Malvaceae) and Diverse Origins of the Polyploid Species (2003, background): “Homology assessment of inversions located in hairpins can be complicated by their frequent and homoplastic appearance within a particular group (Kelchner and Wendel 1996; Kelchner 2000).”
• Phylogenetic Relationships in the Caesalpinioideae (Leguminosae) as Inferred from Chloroplast trnL Intron Sequences (2009, methodology): “Alignments then were verified and modified manually where inconsistencies were found, using as a guideline criteria such as those described by Kelchner (2000).”
• Phylogeny of Nymphaea (Nymphaeaceae): Evidence from Substitutions and Microstructural Changes in the Chloroplast trnT‐trnF Region (2007, background): “Microstructural changes are understood as mutational events that can include one to many nucleotides at once (Gu and Li 1995; Benson 1997; Kelchner 2000).”
• Phylogenetic Analysis of the Plastid Inverted Repeat for 244 Species: Insights into Deeper-Level Angiosperm Relationships from a Long, Slowly Evolving Sequence Region (2011, methodology): “In regions of unambiguous alignment, misaligned indel boundaries in noncoding sequence were shifted according to the criteria of Kelchner (2000).”
• Molecular Phylogenetics, Character Evolution, and Suprageneric Classification of Lamioideae (Lamiaceae)1 (2010, methodology): “Most of the alignments were straightforward; ambiguities due to gaps were solved by following the advice of Kelchner (2000).”
• Highly Variable Chloroplast Markers for Evaluating Plant Phylogeny at Low Taxonomic Levels and for DNA Barcoding (2012, background): “Several authors have suggested ways to interpret the informative but problematic characters [38,39].”
• Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA (2009, background): “6; Graham and Olmstead 2000; Kelchner 2000; Kelchner and Wendel 1996; Quandt et al. 2003; Löhne and Borsch 2005; Sotiaux et al. 2009).”
• Phylogeny of Hibiscus and the Tribe Hibisceae (Malvaceae) Using Chloroplast DNA Sequences of ndhF and the rpl16 Intron (2002, background): “loop substitution and insertion/deletion bias in introns [Kelchner 2000]), we can have increased confidence that the topologies found accurately reflect the history of the chloroplasts.”
• Phylogeny of basal eudicots: Insights from non-coding and rapidly evolving DNA (2007, background): “Thus, microstructural mutations in rapidly evolving spacers and introns can be expected to be of high phylogenetic utility (Kelchner 2000), as has been shown for indels supporting shallower nodes (Müller and Borsch 2005) as well as for indels in the conserved chloroplast-inverted repeat (Graham et…”
• Phylogenetic Relationships and Chromosome Number Evolution in Passiflora (2006, methodology): “Since indel events are frequent occurrences in chloroplast non-coding regions (Kelchner 2000), removing the resulting gap regions from the analysis reduced the number of informative characters by 18%.”