Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA

By Thomas Borsch, D. Quandt. Plant Systematics and Evolution, 2009

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West to east dispersal and subsequent rapid diversification of the mega‐diverse genus Begonia (Begoniaceae) in the Malesian archipelago (2012, background): “Nineteen mutational hotspots, most of which were length differences of homonucleotide strands, together c. 5.1% of the aligned positions, were excluded from the final matrix because of uncertain homology (Kelchner, 2000; Borsch & Quandt, 2009).”
Highly Variable Chloroplast Markers for Evaluating Plant Phylogeny at Low Taxonomic Levels and for DNA Barcoding (2012, background): “Most of the loci identified in this study have been used frequently for phylogenetic reconstructions, and their evolutionary features have been discussed [24,26,27].”
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): “Inversions are frequently encountered in noncoding regions of plastid DNA (Graham et al. 2000; Borsch and Quandt 2009), and consequently all 40 individual region alignments were thoroughly searched at least twice by eye for inversions, which were reversed and complemented before analysis.”