Nucleotide substitution rates in legume chloroplast DNA depend on the presence of the inverted repeat.

By A. Perry, Kenneth H. Wolfe. 2002

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A Comparative Analysis of Whole Plastid Genomes from the Apiales: Expansion and Contraction of the Inverted Repeat, Mitochondrial to Plastid Transfer of DNA, and Identification of Highly Divergent Noncoding Regions (2015, background): “…to provide fewer variable characters than noncoding regions; similarly, all regions contained in the IR were also excluded because many of them diverge at slower rates compared to sequences located in their adjacent single-copy regions (Wolfe et al. 1987; Perry and Wolfe 2002; Kim and Lee 2004).”
Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. (2007, background): “…of this investigation was to identify rapidly evolving regions of the chloroplast genome and the inverted repeats have been shown to accumulate mutations at a slower rate than the single-copy regions (Perry and Wolfe, 2002), our effort focused on the single-copy regions of the chloroplast genome.”