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Premise of the study:  Predictable chloroplast DNA (cpDNA) sequences have been listed for the shallowest taxonomic studies in plants. We investigated whether plastid regions that vary between closely allied species could be applied for intraspecific studies and compared the variation of these plastid segments with two nuclear regions.    Methods:  We screened 16 plastid and two nuclear intronic regions for species of the genus  Cereus  (Cactaceae) at three hierarchical levels (species from different clades, species of the same clade, and allopatric populations).    Results:  Ten plastid regions presented interspecific variation, and six of them showed variation at the intraspecific level. The two nuclear regions showed both inter‐ and intraspecific variation, and in general they showed higher levels of variability in almost all hierarchical levels than the plastid segments.    Discussion:  Our data suggest no correspondence between variation of plastid regions at the interspecific and intraspecific level, probably due to lineage‐specific variation in cpDNA, which appears to have less effect in nuclear data. Despite the heterogeneity in evolutionary rates of cpDNA, we highlight three plastid segments that may be considered in initial screenings in plant phylogeographic studies.

Lineage‐specific evolutionary rate in plants: Contributions of a screening for Cereus (Cactaceae)